diff --git a/.github/workflows/package-release.yml b/.github/workflows/package-release.yml
index fecb0166d..38d80908d 100644
--- a/.github/workflows/package-release.yml
+++ b/.github/workflows/package-release.yml
@@ -129,6 +129,21 @@ jobs:
           fetch-depth: 0
           ref: ${{ github.event.inputs.branch }}
           persist-credentials: false
+      - name: Python | Setup
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.9'
+      - name: Python | Install bump2version
+        run: |
+          python -m pip install --upgrade pip
+          pip install bump2version
+      - name: Python | Bump Version Release
+        id: bump_version
+        run: |
+          cur_dir=$GITHUB_WORKSPACE
+          cd ${{ matrix.package_dir }}
+          bump2version release --no-commit --allow-dirty
+          cd ${cur_dir}
       - name: Docker | Tag
         id: docker_tag
         run: |
diff --git a/.github/workflows/pre-release-filter.yml b/.github/workflows/pre-release-filter.yml
index 0070ad0a6..c46383f91 100644
--- a/.github/workflows/pre-release-filter.yml
+++ b/.github/workflows/pre-release-filter.yml
@@ -37,9 +37,6 @@ jobs:
           PACKAGE_DIRS=""
           COMPANION_FILES="VERSION .bumpversion.cfg"
 
-          # TODO: Remove this line and its effects after debugging
-          ALLOWED_DIRS="segmentation/imagej-threshold-apply-tool segmentation/imagej-threshold-huang-tool"
-
           # Get the names of all the files tracked by git in the repo
           ALL_FILES=$(git ls-tree --full-tree -r --name-only HEAD)
 
@@ -54,13 +51,6 @@ jobs:
               continue
             fi
 
-            # Check if the package directory is allowed
-            if [[ ! "$ALLOWED_DIRS" == *"$pkg_dir"* ]]
-            then
-              echo "Skipping $pkg_dir"
-              continue
-            fi
-
             # Check if the file is a pyproject.toml file
             if [[ "$(basename ${file})" = *"pyproject"* ]]
             then
diff --git a/clustering/k-means-clustering-tool/Dockerfile b/clustering/k-means-clustering-tool/Dockerfile
index 6d8db17a8..1d0d53a9e 100644
--- a/clustering/k-means-clustering-tool/Dockerfile
+++ b/clustering/k-means-clustering-tool/Dockerfile
@@ -9,12 +9,17 @@ ENV POLUS_LOG="INFO"
 # Work directory defined in the base container
 WORKDIR ${EXEC_DIR}
 
-COPY pyproject.toml ${EXEC_DIR}
-COPY VERSION ${EXEC_DIR}
-COPY README.md ${EXEC_DIR}
-COPY src ${EXEC_DIR}/src
+# TODO: Change the tool_dir to the tool directory
+ENV TOOL_DIR="clustering/k-means-clustering-tool"
 
-RUN pip3 install ${EXEC_DIR} --no-cache-dir
+# Copy the repository into the container
+RUN mkdir image-tools
+COPY . ${EXEC_DIR}/image-tools
 
-ENTRYPOINT ["python3", "-m", "polus.images.clustering.k_means"]
+# Install the tool
+RUN pip3 install "${EXEC_DIR}/image-tools/${TOOL_DIR}" --no-cache-dir
+
+# Set the entrypoint
+# TODO: Change the entrypoint to the tool entrypoint
+ENTRYPOINT ["python3", "-m", "polus.images.clustering.k_means_clustering"]
 CMD ["--help"]
diff --git a/clustering/k-means-clustering-tool/build-docker.sh b/clustering/k-means-clustering-tool/build-docker.sh
index 275ef5941..4dedab2f6 100644
--- a/clustering/k-means-clustering-tool/build-docker.sh
+++ b/clustering/k-means-clustering-tool/build-docker.sh
@@ -1,4 +1,23 @@
+
 #!/bin/bash
 
+# Change the name of the tool here
+tool_dir="clustering"
+tool_name="k-means-clustering-tool"
+
+# The version is read from the VERSION file
 version=$(<VERSION)
-docker build . -t polusai/k-means-clustering-tool:${version}
+tag="polusai/${tool_name}:${version}"
+echo "Building docker image with tag: ${tag}"
+
+# The current directory and the repository root are saved in variables
+cur_dir=$(pwd)
+repo_root=$(git rev-parse --show-toplevel)
+
+# The Dockerfile and .dockerignore files are copied to the repository root before building the image
+cd ${repo_root}
+cp ./${tool_dir}/${tool_name}/Dockerfile .
+cp .gitingore .dockerignore
+docker build . -t ${tag}
+rm Dockerfile .dockerignore
+cd ${cur_dir}
diff --git a/clustering/outlier-removal-tool/Dockerfile b/clustering/outlier-removal-tool/Dockerfile
index da498532b..3aacb378b 100644
--- a/clustering/outlier-removal-tool/Dockerfile
+++ b/clustering/outlier-removal-tool/Dockerfile
@@ -4,17 +4,22 @@ FROM polusai/bfio:2.3.3
 ENV EXEC_DIR="/opt/executables"
 ENV POLUS_IMG_EXT=".ome.tif"
 ENV POLUS_TAB_EXT=".arrow"
-
+ENV POLUS_LOG="INFO"
 
 # Work directory defined in the base container
 WORKDIR ${EXEC_DIR}
 
-COPY pyproject.toml ${EXEC_DIR}
-COPY VERSION ${EXEC_DIR}
-COPY README.md ${EXEC_DIR}
+# TODO: Change the tool_dir to the tool directory
+ENV TOOL_DIR="clustering/outlier-removal-tool"
 
-RUN pip3 install ${EXEC_DIR} --no-cache
+# Copy the repository into the container
+RUN mkdir image-tools
+COPY . ${EXEC_DIR}/image-tools
 
+# Install the tool
+RUN pip3 install "${EXEC_DIR}/image-tools/${TOOL_DIR}" --no-cache-dir
 
+# Set the entrypoint
+# TODO: Change the entrypoint to the tool entrypoint
 ENTRYPOINT ["python3", "-m", "polus.images.clustering.outlier_removal"]
 CMD ["--help"]
diff --git a/clustering/outlier-removal-tool/build-docker.sh b/clustering/outlier-removal-tool/build-docker.sh
index be64f7228..3d1dfe86e 100644
--- a/clustering/outlier-removal-tool/build-docker.sh
+++ b/clustering/outlier-removal-tool/build-docker.sh
@@ -1,4 +1,23 @@
+
 #!/bin/bash
 
+# Change the name of the tool here
+tool_dir="clustering"
+tool_name="outlier-removal-tool"
+
+# The version is read from the VERSION file
 version=$(<VERSION)
-docker build . -t polusai/outlier-removal-tool:${version}
+tag="polusai/${tool_name}:${version}"
+echo "Building docker image with tag: ${tag}"
+
+# The current directory and the repository root are saved in variables
+cur_dir=$(pwd)
+repo_root=$(git rev-parse --show-toplevel)
+
+# The Dockerfile and .dockerignore files are copied to the repository root before building the image
+cd ${repo_root}
+cp ./${tool_dir}/${tool_name}/Dockerfile .
+cp .gitingore .dockerignore
+docker build . -t ${tag}
+rm Dockerfile .dockerignore
+cd ${cur_dir}
diff --git a/features/nyxus-tool/Dockerfile b/features/nyxus-tool/Dockerfile
index 172618817..9b2455010 100755
--- a/features/nyxus-tool/Dockerfile
+++ b/features/nyxus-tool/Dockerfile
@@ -4,16 +4,22 @@ FROM polusai/bfio:2.3.3
 ENV EXEC_DIR="/opt/executables"
 ENV POLUS_IMG_EXT=".ome.tif"
 ENV POLUS_TAB_EXT=".csv"
+ENV POLUS_LOG="INFO"
 
 # Work directory defined in the base container
 WORKDIR ${EXEC_DIR}
 
-COPY pyproject.toml ${EXEC_DIR}
-COPY VERSION ${EXEC_DIR}
-COPY README.md ${EXEC_DIR}
-COPY src ${EXEC_DIR}/src
+# TODO: Change the tool_dir to the tool directory
+ENV TOOL_DIR="features/nyxus-tool"
 
-RUN pip3 install ${EXEC_DIR} --no-cache-dir
+# Copy the repository into the container
+RUN mkdir image-tools
+COPY . ${EXEC_DIR}/image-tools
 
-ENTRYPOINT ["python3", "-m", "polus.images.features.nyxus_plugin"]
+# Install the tool
+RUN pip3 install "${EXEC_DIR}/image-tools/${TOOL_DIR}" --no-cache-dir
+
+# Set the entrypoint
+# TODO: Change the entrypoint to the tool entrypoint
+ENTRYPOINT ["python3", "-m", "polus.images.features.nyxus"]
 CMD ["--help"]
diff --git a/features/nyxus-tool/build-docker.sh b/features/nyxus-tool/build-docker.sh
index c7a24dddd..368b772f2 100755
--- a/features/nyxus-tool/build-docker.sh
+++ b/features/nyxus-tool/build-docker.sh
@@ -1,4 +1,23 @@
+
 #!/bin/bash
 
+# Change the name of the tool here
+tool_dir="features"
+tool_name="nyxus-tool"
+
+# The version is read from the VERSION file
 version=$(<VERSION)
-docker build . -t polusai/nyxus-tool:${version}
+tag="polusai/${tool_name}:${version}"
+echo "Building docker image with tag: ${tag}"
+
+# The current directory and the repository root are saved in variables
+cur_dir=$(pwd)
+repo_root=$(git rev-parse --show-toplevel)
+
+# The Dockerfile and .dockerignore files are copied to the repository root before building the image
+cd ${repo_root}
+cp ./${tool_dir}/${tool_name}/Dockerfile .
+cp .gitingore .dockerignore
+docker build . -t ${tag}
+rm Dockerfile .dockerignore
+cd ${cur_dir}
diff --git a/features/pixel-segmentation-eval-tool/Dockerfile b/features/pixel-segmentation-eval-tool/Dockerfile
index 578bc68bd..d3e1b930d 100644
--- a/features/pixel-segmentation-eval-tool/Dockerfile
+++ b/features/pixel-segmentation-eval-tool/Dockerfile
@@ -4,16 +4,22 @@ FROM polusai/bfio:2.1.9
 ENV EXEC_DIR="/opt/executables"
 ENV POLUS_IMG_EXT=".ome.tif"
 ENV POLUS_TAB_EXT=".csv"
+ENV POLUS_LOG="INFO"
 
 # Work directory defined in the base container
 WORKDIR ${EXEC_DIR}
 
-COPY pyproject.toml ${EXEC_DIR}
-COPY VERSION ${EXEC_DIR}
-COPY README.md ${EXEC_DIR}
-COPY src ${EXEC_DIR}/src
+# TODO: Change the tool_dir to the tool directory
+ENV TOOL_DIR="features/pixel-segmentation-eval-tool"
 
-RUN pip3 install ${EXEC_DIR} --no-cache-dir
+# Copy the repository into the container
+RUN mkdir image-tools
+COPY . ${EXEC_DIR}/image-tools
 
+# Install the tool
+RUN pip3 install "${EXEC_DIR}/image-tools/${TOOL_DIR}" --no-cache-dir
+
+# Set the entrypoint
+# TODO: Change the entrypoint to the tool entrypoint
 ENTRYPOINT ["python3", "-m", "polus.images.features.pixel_segmentation_eval"]
 CMD ["--help"]
diff --git a/features/pixel-segmentation-eval-tool/build-docker.sh b/features/pixel-segmentation-eval-tool/build-docker.sh
index 364f9c4a0..5ae8d83cb 100644
--- a/features/pixel-segmentation-eval-tool/build-docker.sh
+++ b/features/pixel-segmentation-eval-tool/build-docker.sh
@@ -1,4 +1,23 @@
+
 #!/bin/bash
 
+# Change the name of the tool here
+tool_dir="features"
+tool_name="pixel-segmentation-eval-tool"
+
+# The version is read from the VERSION file
 version=$(<VERSION)
-docker build . -t polusai/pixel-segmentation-eval-tool:${version}
+tag="polusai/${tool_name}:${version}"
+echo "Building docker image with tag: ${tag}"
+
+# The current directory and the repository root are saved in variables
+cur_dir=$(pwd)
+repo_root=$(git rev-parse --show-toplevel)
+
+# The Dockerfile and .dockerignore files are copied to the repository root before building the image
+cd ${repo_root}
+cp ./${tool_dir}/${tool_name}/Dockerfile .
+cp .gitingore .dockerignore
+docker build . -t ${tag}
+rm Dockerfile .dockerignore
+cd ${cur_dir}
diff --git a/features/region-segmentation-eval-tool/Dockerfile b/features/region-segmentation-eval-tool/Dockerfile
index 9a32afb4c..274a77cef 100644
--- a/features/region-segmentation-eval-tool/Dockerfile
+++ b/features/region-segmentation-eval-tool/Dockerfile
@@ -4,16 +4,22 @@ FROM polusai/bfio:2.1.9
 ENV EXEC_DIR="/opt/executables"
 ENV POLUS_IMG_EXT=".ome.tif"
 ENV POLUS_TAB_EXT=".csv"
+ENV POLUS_LOG="INFO"
 
 # Work directory defined in the base container
 WORKDIR ${EXEC_DIR}
 
-COPY pyproject.toml ${EXEC_DIR}
-COPY VERSION ${EXEC_DIR}
-COPY README.md ${EXEC_DIR}
-COPY src ${EXEC_DIR}/src
+# TODO: Change the tool_dir to the tool directory
+ENV TOOL_DIR="features/region-segmentation-eval-tool"
 
-RUN pip3 install ${EXEC_DIR} --no-cache-dir
+# Copy the repository into the container
+RUN mkdir image-tools
+COPY . ${EXEC_DIR}/image-tools
 
+# Install the tool
+RUN pip3 install "${EXEC_DIR}/image-tools/${TOOL_DIR}" --no-cache-dir
+
+# Set the entrypoint
+# TODO: Change the entrypoint to the tool entrypoint
 ENTRYPOINT ["python3", "-m", "polus.images.features.region_segmentation_eval"]
 CMD ["--help"]
diff --git a/features/region-segmentation-eval-tool/build-docker.sh b/features/region-segmentation-eval-tool/build-docker.sh
index 1b60a2101..9c788beb5 100644
--- a/features/region-segmentation-eval-tool/build-docker.sh
+++ b/features/region-segmentation-eval-tool/build-docker.sh
@@ -1,4 +1,23 @@
+
 #!/bin/bash
 
+# Change the name of the tool here
+tool_dir="features"
+tool_name="region-segmentation-eval-tool"
+
+# The version is read from the VERSION file
 version=$(<VERSION)
-docker build . -t polusai/region-segmentation-eval-tool:${version}
+tag="polusai/${tool_name}:${version}"
+echo "Building docker image with tag: ${tag}"
+
+# The current directory and the repository root are saved in variables
+cur_dir=$(pwd)
+repo_root=$(git rev-parse --show-toplevel)
+
+# The Dockerfile and .dockerignore files are copied to the repository root before building the image
+cd ${repo_root}
+cp ./${tool_dir}/${tool_name}/Dockerfile .
+cp .gitingore .dockerignore
+docker build . -t ${tag}
+rm Dockerfile .dockerignore
+cd ${cur_dir}
diff --git a/formats/arrow-to-tabular-tool/Dockerfile b/formats/arrow-to-tabular-tool/Dockerfile
index 210b38a63..bba2b8535 100644
--- a/formats/arrow-to-tabular-tool/Dockerfile
+++ b/formats/arrow-to-tabular-tool/Dockerfile
@@ -4,17 +4,22 @@ FROM polusai/bfio:2.1.9
 ENV EXEC_DIR="/opt/executables"
 ENV POLUS_IMG_EXT=".ome.tif"
 ENV POLUS_TAB_EXT=".csv"
+ENV POLUS_LOG="INFO"
 
 # Work directory defined in the base container
 WORKDIR ${EXEC_DIR}
 
-COPY pyproject.toml ${EXEC_DIR}
-COPY VERSION ${EXEC_DIR}
-COPY README.md ${EXEC_DIR}
-RUN pip3 install --index-url https://test.pypi.org/simple/ filepattern==2.2.7
-COPY src ${EXEC_DIR}/src
+# TODO: Change the tool_dir to the tool directory
+ENV TOOL_DIR="formats/arrow-to-tabular-tool"
 
-RUN pip3 install ${EXEC_DIR} --no-cache-dir
+# Copy the repository into the container
+RUN mkdir image-tools
+COPY . ${EXEC_DIR}/image-tools
 
+# Install the tool
+RUN pip3 install "${EXEC_DIR}/image-tools/${TOOL_DIR}" --no-cache-dir
+
+# Set the entrypoint
+# TODO: Change the entrypoint to the tool entrypoint
 ENTRYPOINT ["python3", "-m", "polus.images.formats.arrow_to_tabular"]
 CMD ["--help"]
diff --git a/formats/arrow-to-tabular-tool/build-docker.sh b/formats/arrow-to-tabular-tool/build-docker.sh
index b1ddde0d0..f75e537e8 100755
--- a/formats/arrow-to-tabular-tool/build-docker.sh
+++ b/formats/arrow-to-tabular-tool/build-docker.sh
@@ -1,4 +1,23 @@
+
 #!/bin/bash
 
+# Change the name of the tool here
+tool_dir="formats"
+tool_name="arrow-to-tabular-tool"
+
+# The version is read from the VERSION file
 version=$(<VERSION)
-docker build . -t polusai/arrow-to-tabular-tool:${version}
+tag="polusai/${tool_name}:${version}"
+echo "Building docker image with tag: ${tag}"
+
+# The current directory and the repository root are saved in variables
+cur_dir=$(pwd)
+repo_root=$(git rev-parse --show-toplevel)
+
+# The Dockerfile and .dockerignore files are copied to the repository root before building the image
+cd ${repo_root}
+cp ./${tool_dir}/${tool_name}/Dockerfile .
+cp .gitingore .dockerignore
+docker build . -t ${tag}
+rm Dockerfile .dockerignore
+cd ${cur_dir}
diff --git a/formats/file-renaming-tool/Dockerfile b/formats/file-renaming-tool/Dockerfile
index 582884d42..e7abbba30 100644
--- a/formats/file-renaming-tool/Dockerfile
+++ b/formats/file-renaming-tool/Dockerfile
@@ -2,19 +2,24 @@ FROM polusai/bfio:2.1.9
 
 # environment variables defined in polusai/bfio
 ENV EXEC_DIR="/opt/executables"
-ENV POLUS_LOG="INFO"
 ENV POLUS_IMG_EXT=".ome.tif"
 ENV POLUS_TAB_EXT=".csv"
+ENV POLUS_LOG="INFO"
 
 # Work directory defined in the base container
 WORKDIR ${EXEC_DIR}
 
-COPY pyproject.toml ${EXEC_DIR}
-COPY VERSION ${EXEC_DIR}
-COPY README.md ${EXEC_DIR}
-COPY src ${EXEC_DIR}/src
+# TODO: Change the tool_dir to the tool directory
+ENV TOOL_DIR="formats/file-renaming-tool"
+
+# Copy the repository into the container
+RUN mkdir image-tools
+COPY . ${EXEC_DIR}/image-tools
 
-RUN pip3 install ${EXEC_DIR} --no-cache-dir
+# Install the tool
+RUN pip3 install "${EXEC_DIR}/image-tools/${TOOL_DIR}" --no-cache-dir
 
+# Set the entrypoint
+# TODO: Change the entrypoint to the tool entrypoint
 ENTRYPOINT ["python3", "-m", "polus.images.formats.file_renaming"]
 CMD ["--help"]
diff --git a/formats/file-renaming-tool/build-docker.sh b/formats/file-renaming-tool/build-docker.sh
index 916255e60..4c1cb3a73 100644
--- a/formats/file-renaming-tool/build-docker.sh
+++ b/formats/file-renaming-tool/build-docker.sh
@@ -1,3 +1,23 @@
+
 #!/bin/bash
+
+# Change the name of the tool here
+tool_dir="formats"
+tool_name="file-renaming-tool"
+
+# The version is read from the VERSION file
 version=$(<VERSION)
-docker build . -t polusai/file-renaming-tool:${version}
+tag="polusai/${tool_name}:${version}"
+echo "Building docker image with tag: ${tag}"
+
+# The current directory and the repository root are saved in variables
+cur_dir=$(pwd)
+repo_root=$(git rev-parse --show-toplevel)
+
+# The Dockerfile and .dockerignore files are copied to the repository root before building the image
+cd ${repo_root}
+cp ./${tool_dir}/${tool_name}/Dockerfile .
+cp .gitingore .dockerignore
+docker build . -t ${tag}
+rm Dockerfile .dockerignore
+cd ${cur_dir}
diff --git a/formats/label-to-vector-tool/Dockerfile b/formats/label-to-vector-tool/Dockerfile
index c2a4931f4..911c3bfc7 100644
--- a/formats/label-to-vector-tool/Dockerfile
+++ b/formats/label-to-vector-tool/Dockerfile
@@ -2,22 +2,24 @@ FROM polusai/bfio:2.1.9
 
 # environment variables defined in polusai/bfio
 ENV EXEC_DIR="/opt/executables"
-ENV DATA_DIR="/data"
-ENV POLUS_LOG="INFO"
 ENV POLUS_IMG_EXT=".ome.tif"
 ENV POLUS_TAB_EXT=".csv"
+ENV POLUS_LOG="INFO"
 
 # Work directory defined in the base container
-RUN mkdir ${EXEC_DIR}/label-to-vector-plugin
-ENV EXEC_DIR="${EXEC_DIR}/label-to-vector-plugin"
 WORKDIR ${EXEC_DIR}
 
-COPY pyproject.toml ${EXEC_DIR}
-COPY VERSION ${EXEC_DIR}
-COPY README.md ${EXEC_DIR}
-COPY src ${EXEC_DIR}/src
+# TODO: Change the tool_dir to the tool directory
+ENV TOOL_DIR="formats/label-to-vector-tool"
+
+# Copy the repository into the container
+RUN mkdir image-tools
+COPY . ${EXEC_DIR}/image-tools
 
-RUN pip3 install ${EXEC_DIR} --no-cache-dir
+# Install the tool
+RUN pip3 install "${EXEC_DIR}/image-tools/${TOOL_DIR}" --no-cache-dir
 
+# Set the entrypoint
+# TODO: Change the entrypoint to the tool entrypoint
 ENTRYPOINT ["python3", "-m", "polus.images.formats.label_to_vector"]
 CMD ["--help"]
diff --git a/formats/label-to-vector-tool/build-docker.sh b/formats/label-to-vector-tool/build-docker.sh
index 8723ec346..0664fa4b0 100755
--- a/formats/label-to-vector-tool/build-docker.sh
+++ b/formats/label-to-vector-tool/build-docker.sh
@@ -1,4 +1,23 @@
+
 #!/bin/bash
 
+# Change the name of the tool here
+tool_dir="formats"
+tool_name="label-to-vector-tool"
+
+# The version is read from the VERSION file
 version=$(<VERSION)
-docker build . -t polusai/label-to-vector-tool:"${version}"
+tag="polusai/${tool_name}:${version}"
+echo "Building docker image with tag: ${tag}"
+
+# The current directory and the repository root are saved in variables
+cur_dir=$(pwd)
+repo_root=$(git rev-parse --show-toplevel)
+
+# The Dockerfile and .dockerignore files are copied to the repository root before building the image
+cd ${repo_root}
+cp ./${tool_dir}/${tool_name}/Dockerfile .
+cp .gitingore .dockerignore
+docker build . -t ${tag}
+rm Dockerfile .dockerignore
+cd ${cur_dir}
diff --git a/formats/ome-converter-tool/Dockerfile b/formats/ome-converter-tool/Dockerfile
index e35be14c9..088c8b643 100644
--- a/formats/ome-converter-tool/Dockerfile
+++ b/formats/ome-converter-tool/Dockerfile
@@ -9,12 +9,17 @@ ENV POLUS_LOG="INFO"
 # Work directory defined in the base container
 WORKDIR ${EXEC_DIR}
 
-COPY pyproject.toml ${EXEC_DIR}
-COPY VERSION ${EXEC_DIR}
-COPY README.md ${EXEC_DIR}
-COPY src ${EXEC_DIR}/src
+# TODO: Change the tool_dir to the tool directory
+ENV TOOL_DIR="formats/ome-converter-tool"
 
-RUN pip3 install ${EXEC_DIR} --no-cache-dir
+# Copy the repository into the container
+RUN mkdir image-tools
+COPY . ${EXEC_DIR}/image-tools
 
+# Install the tool
+RUN pip3 install "${EXEC_DIR}/image-tools/${TOOL_DIR}" --no-cache-dir
+
+# Set the entrypoint
+# TODO: Change the entrypoint to the tool entrypoint
 ENTRYPOINT ["python3", "-m", "polus.images.formats.ome_converter"]
 CMD ["--help"]
diff --git a/formats/ome-converter-tool/build-docker.sh b/formats/ome-converter-tool/build-docker.sh
index 5d3ba149e..8755972ac 100755
--- a/formats/ome-converter-tool/build-docker.sh
+++ b/formats/ome-converter-tool/build-docker.sh
@@ -1,4 +1,23 @@
+
 #!/bin/bash
 
+# Change the name of the tool here
+tool_dir="formats"
+tool_name="ome-converter-tool"
+
+# The version is read from the VERSION file
 version=$(<VERSION)
-docker build . -t polusai/ome-converter-tool:${version}
+tag="polusai/${tool_name}:${version}"
+echo "Building docker image with tag: ${tag}"
+
+# The current directory and the repository root are saved in variables
+cur_dir=$(pwd)
+repo_root=$(git rev-parse --show-toplevel)
+
+# The Dockerfile and .dockerignore files are copied to the repository root before building the image
+cd ${repo_root}
+cp ./${tool_dir}/${tool_name}/Dockerfile .
+cp .gitingore .dockerignore
+docker build . -t ${tag}
+rm Dockerfile .dockerignore
+cd ${cur_dir}
diff --git a/formats/vector-to-label-tool/Dockerfile b/formats/vector-to-label-tool/Dockerfile
index 37c55784a..63d36955f 100644
--- a/formats/vector-to-label-tool/Dockerfile
+++ b/formats/vector-to-label-tool/Dockerfile
@@ -1,25 +1,25 @@
 FROM polusai/label-to-vector-plugin:0.7.0-dev30
 
 # environment variables defined in polusai/bfio
-# ENV EXEC_DIR="/opt/executables"
-# ENV DATA_DIR="/data"
-# ENV POLUS_LOG="INFO"
-# ENV POLUS_IMG_EXT=".ome.tif"
-# ENV POLUS_TAB_EXT=".csv"
+ENV EXEC_DIR="/opt/executables"
+ENV POLUS_IMG_EXT=".ome.tif"
+ENV POLUS_TAB_EXT=".csv"
+ENV POLUS_LOG="INFO"
 
 # Work directory defined in the base container
-
-ENV EXEC_DIR="${EXEC_DIR}/../vector-to-label-plugin"
-RUN mkdir ${EXEC_DIR}
-
 WORKDIR ${EXEC_DIR}
 
-COPY pyproject.toml ${EXEC_DIR}
-COPY VERSION ${EXEC_DIR}
-COPY README.md ${EXEC_DIR}
-COPY src ${EXEC_DIR}/src
+# TODO: Change the tool_dir to the tool directory
+ENV TOOL_DIR="formats/vector-to-label-tool"
+
+# Copy the repository into the container
+RUN mkdir image-tools
+COPY . ${EXEC_DIR}/image-tools
 
-RUN pip3 install ${EXEC_DIR} --no-cache-dir
+# Install the tool
+RUN pip3 install "${EXEC_DIR}/image-tools/${TOOL_DIR}" --no-cache-dir
 
+# Set the entrypoint
+# TODO: Change the entrypoint to the tool entrypoint
 ENTRYPOINT ["python3", "-m", "polus.images.formats.vector_to_label"]
 CMD ["--help"]
diff --git a/formats/vector-to-label-tool/build-docker.sh b/formats/vector-to-label-tool/build-docker.sh
index 30e968b5d..03332c35d 100755
--- a/formats/vector-to-label-tool/build-docker.sh
+++ b/formats/vector-to-label-tool/build-docker.sh
@@ -1,4 +1,23 @@
+
 #!/bin/bash
 
+# Change the name of the tool here
+tool_dir="formats"
+tool_name="vector-to-label-tool"
+
+# The version is read from the VERSION file
 version=$(<VERSION)
-docker build . -t polusai/vector-to-label-tool:"${version}"
+tag="polusai/${tool_name}:${version}"
+echo "Building docker image with tag: ${tag}"
+
+# The current directory and the repository root are saved in variables
+cur_dir=$(pwd)
+repo_root=$(git rev-parse --show-toplevel)
+
+# The Dockerfile and .dockerignore files are copied to the repository root before building the image
+cd ${repo_root}
+cp ./${tool_dir}/${tool_name}/Dockerfile .
+cp .gitingore .dockerignore
+docker build . -t ${tag}
+rm Dockerfile .dockerignore
+cd ${cur_dir}
diff --git a/regression/basic-flatfield-estimation-tool/Dockerfile b/regression/basic-flatfield-estimation-tool/Dockerfile
index 36884685d..430359de2 100644
--- a/regression/basic-flatfield-estimation-tool/Dockerfile
+++ b/regression/basic-flatfield-estimation-tool/Dockerfile
@@ -27,27 +27,29 @@ RUN apt update && \
 
 # Symbolic link to python3.9
 RUN ln -sf /usr/bin/python3.9 /usr/bin/python3
+RUN mkdir /.cache && chmod 777 /.cache
 
 # environment variables defined in polusai/bfio
 ENV EXEC_DIR="/opt/executables"
-ENV DATA_DIR="/data"
-ENV POLUS_LOG="INFO"
 ENV POLUS_IMG_EXT=".ome.tif"
 ENV POLUS_TAB_EXT=".csv"
-
-RUN mkdir /.cache && chmod 777 /.cache
+ENV POLUS_LOG="INFO"
+ENV DATA_DIR="/data"
 
 # Work directory defined in the base container
 WORKDIR ${EXEC_DIR}
 
-# Copy the python package
-COPY pyproject.toml ${EXEC_DIR}
-COPY VERSION ${EXEC_DIR}
-COPY README.md ${EXEC_DIR}
-COPY src ${EXEC_DIR}/src
+# TODO: Change the tool_dir to the tool directory
+ENV TOOL_DIR="regression/basic-flatfield-estimation-tool"
+
+# Copy the repository into the container
+RUN mkdir image-tools
+COPY . ${EXEC_DIR}/image-tools
 
-# Install the python package
-RUN pip3 install ${EXEC_DIR} --no-cache-dir
+# Install the tool
+RUN pip3 install "${EXEC_DIR}/image-tools/${TOOL_DIR}" --no-cache-dir
 
+# Set the entrypoint
+# TODO: Change the entrypoint to the tool entrypoint
 ENTRYPOINT ["python3", "-m", "polus.images.regression.basic_flatfield_estimation"]
 CMD ["--help"]
diff --git a/regression/basic-flatfield-estimation-tool/build-docker.sh b/regression/basic-flatfield-estimation-tool/build-docker.sh
index 28fe53cce..7b2a8f17e 100755
--- a/regression/basic-flatfield-estimation-tool/build-docker.sh
+++ b/regression/basic-flatfield-estimation-tool/build-docker.sh
@@ -1,4 +1,23 @@
+
 #!/bin/bash
 
+# Change the name of the tool here
+tool_dir="regression"
+tool_name="basic-flatfield-estimation-tool"
+
+# The version is read from the VERSION file
 version=$(<VERSION)
-docker build . -t polusai/basic-flatfield-estimation-tool:"${version}"
+tag="polusai/${tool_name}:${version}"
+echo "Building docker image with tag: ${tag}"
+
+# The current directory and the repository root are saved in variables
+cur_dir=$(pwd)
+repo_root=$(git rev-parse --show-toplevel)
+
+# The Dockerfile and .dockerignore files are copied to the repository root before building the image
+cd ${repo_root}
+cp ./${tool_dir}/${tool_name}/Dockerfile .
+cp .gitingore .dockerignore
+docker build . -t ${tag}
+rm Dockerfile .dockerignore
+cd ${cur_dir}
diff --git a/regression/theia-bleedthrough-estimation-tool/Dockerfile b/regression/theia-bleedthrough-estimation-tool/Dockerfile
index fb7e555c2..58194e57d 100644
--- a/regression/theia-bleedthrough-estimation-tool/Dockerfile
+++ b/regression/theia-bleedthrough-estimation-tool/Dockerfile
@@ -27,27 +27,26 @@ RUN apt update && \
 
 # Symbolic link to python3.9
 RUN ln -sf /usr/bin/python3.9 /usr/bin/python3
+RUN mkdir /.cache && chmod 777 /.cache
 
 # environment variables defined in polusai/bfio
 ENV EXEC_DIR="/opt/executables"
-ENV DATA_DIR="/data"
-ENV POLUS_LOG="INFO"
 ENV POLUS_IMG_EXT=".ome.tif"
 ENV POLUS_TAB_EXT=".csv"
+ENV POLUS_LOG="INFO"
+ENV DATA_DIR="/data"
 
-RUN mkdir /.cache && chmod 777 /.cache
-
-# Work directory defined in the base container
-WORKDIR ${EXEC_DIR}
+# TODO: Change the tool_dir to the tool directory
+ENV TOOL_DIR="regression/theia-bleedthrough-estimation-tool"
 
-# Copy the python package
-COPY pyproject.toml ${EXEC_DIR}
-COPY VERSION ${EXEC_DIR}
-COPY README.md ${EXEC_DIR}
-COPY src ${EXEC_DIR}/src
+# Copy the repository into the container
+RUN mkdir image-tools
+COPY . ${EXEC_DIR}/image-tools
 
-# Install the python package
-RUN pip3 install ${EXEC_DIR} --no-cache-dir
+# Install the tool
+RUN pip3 install "${EXEC_DIR}/image-tools/${TOOL_DIR}" --no-cache-dir
 
+# Set the entrypoint
+# TODO: Change the entrypoint to the tool entrypoint
 ENTRYPOINT ["python3", "-m", "polus.images.regression.theia_bleedthrough_estimation"]
 CMD ["--help"]
diff --git a/regression/theia-bleedthrough-estimation-tool/build-docker.sh b/regression/theia-bleedthrough-estimation-tool/build-docker.sh
index 42f27930f..42ebc07bb 100755
--- a/regression/theia-bleedthrough-estimation-tool/build-docker.sh
+++ b/regression/theia-bleedthrough-estimation-tool/build-docker.sh
@@ -1,4 +1,23 @@
+
 #!/bin/bash
 
+# Change the name of the tool here
+tool_dir="regression"
+tool_name="theia-bleedthrough-estimation-tool"
+
+# The version is read from the VERSION file
 version=$(<VERSION)
-docker build . -t polusai/theia-bleedthrough-estimation-tool:"${version}"
+tag="polusai/${tool_name}:${version}"
+echo "Building docker image with tag: ${tag}"
+
+# The current directory and the repository root are saved in variables
+cur_dir=$(pwd)
+repo_root=$(git rev-parse --show-toplevel)
+
+# The Dockerfile and .dockerignore files are copied to the repository root before building the image
+cd ${repo_root}
+cp ./${tool_dir}/${tool_name}/Dockerfile .
+cp .gitingore .dockerignore
+docker build . -t ${tag}
+rm Dockerfile .dockerignore
+cd ${cur_dir}
diff --git a/segmentation/cell-border-segmentation-tool/Dockerfile b/segmentation/cell-border-segmentation-tool/Dockerfile
index 50b22f96c..d963ef2cb 100644
--- a/segmentation/cell-border-segmentation-tool/Dockerfile
+++ b/segmentation/cell-border-segmentation-tool/Dockerfile
@@ -9,14 +9,17 @@ ENV POLUS_LOG="INFO"
 # Work directory defined in the base container
 WORKDIR ${EXEC_DIR}
 
-COPY pyproject.toml ${EXEC_DIR}
-COPY VERSION ${EXEC_DIR}
-COPY README.md ${EXEC_DIR}
-COPY CHANGELOG.md ${EXEC_DIR}
-COPY src ${EXEC_DIR}/src
+# TODO: Change the tool_dir to the tool directory
+ENV TOOL_DIR="segmentation/cell-border-segmentation-tool"
 
-RUN pip3 install ${EXEC_DIR} --no-cache-dir
+# Copy the repository into the container
+RUN mkdir image-tools
+COPY . ${EXEC_DIR}/image-tools
 
-# Default command. Additional arguments are provided through the command line
+# Install the tool
+RUN pip3 install "${EXEC_DIR}/image-tools/${TOOL_DIR}" --no-cache-dir
+
+# Set the entrypoint
+# TODO: Change the entrypoint to the tool entrypoint
 ENTRYPOINT ["python3", "-m", "polus.images.segmentation.cell_border_segmentation"]
 CMD ["--help"]
diff --git a/segmentation/cell-border-segmentation-tool/build-docker.sh b/segmentation/cell-border-segmentation-tool/build-docker.sh
index 2aceab995..eef8c8e08 100755
--- a/segmentation/cell-border-segmentation-tool/build-docker.sh
+++ b/segmentation/cell-border-segmentation-tool/build-docker.sh
@@ -1,4 +1,23 @@
+
 #!/bin/bash
 
+# Change the name of the tool here
+tool_dir="segmentation"
+tool_name="cell-border-segmentation-tool"
+
+# The version is read from the VERSION file
 version=$(<VERSION)
-docker build . -t polusai/cell-border-segmentation-tool:${version}
+tag="polusai/${tool_name}:${version}"
+echo "Building docker image with tag: ${tag}"
+
+# The current directory and the repository root are saved in variables
+cur_dir=$(pwd)
+repo_root=$(git rev-parse --show-toplevel)
+
+# The Dockerfile and .dockerignore files are copied to the repository root before building the image
+cd ${repo_root}
+cp ./${tool_dir}/${tool_name}/Dockerfile .
+cp .gitingore .dockerignore
+docker build . -t ${tag}
+rm Dockerfile .dockerignore
+cd ${cur_dir}
diff --git a/segmentation/imagej-threshold-apply-tool/.bumpversion.cfg b/segmentation/imagej-threshold-apply-tool/.bumpversion.cfg
index d303a602c..2267f56f8 100644
--- a/segmentation/imagej-threshold-apply-tool/.bumpversion.cfg
+++ b/segmentation/imagej-threshold-apply-tool/.bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.5.0
+current_version = 0.5.1-dev0
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<dev>\d+))?
diff --git a/segmentation/imagej-threshold-apply-tool/README.md b/segmentation/imagej-threshold-apply-tool/README.md
index dffe32f21..1598ef49d 100644
--- a/segmentation/imagej-threshold-apply-tool/README.md
+++ b/segmentation/imagej-threshold-apply-tool/README.md
@@ -1,4 +1,4 @@
-# ImageJ threshold apply (v0.5.0)
+# ImageJ threshold apply (v0.5.1-dev0)
 
 This plugin applies a constant manual threshold value to an input collection.
 (Thresholding)[https://en.wikipedia.org/wiki/Thresholding_(image_processing)] converts all pixel values in an image to either 1 or 0 depending on
diff --git a/segmentation/imagej-threshold-apply-tool/VERSION b/segmentation/imagej-threshold-apply-tool/VERSION
index 8f0916f76..6f9bb2cc0 100644
--- a/segmentation/imagej-threshold-apply-tool/VERSION
+++ b/segmentation/imagej-threshold-apply-tool/VERSION
@@ -1 +1 @@
-0.5.0
+0.5.1-dev0
diff --git a/segmentation/imagej-threshold-apply-tool/build-docker.sh b/segmentation/imagej-threshold-apply-tool/build-docker.sh
index f56879000..a7bcca74f 100755
--- a/segmentation/imagej-threshold-apply-tool/build-docker.sh
+++ b/segmentation/imagej-threshold-apply-tool/build-docker.sh
@@ -1,3 +1,4 @@
+
 #!/bin/bash
 
 # Change the name of the tool here
diff --git a/segmentation/imagej-threshold-apply-tool/plugin.json b/segmentation/imagej-threshold-apply-tool/plugin.json
index 7086b1642..9b1e6a8f7 100644
--- a/segmentation/imagej-threshold-apply-tool/plugin.json
+++ b/segmentation/imagej-threshold-apply-tool/plugin.json
@@ -1,6 +1,6 @@
 {
   "name": "ImageJ threshold apply",
-  "version": "0.5.0",
+  "version": "0.5.1-dev0",
   "title": "ImageJ threshold apply",
   "description": "This plugin applies a constant or manual threshold to an input collection.",
   "author": "Nick Schaub (nick.schaub@nih.gov), Anjali Taneja, Benjamin Houghton (benjamin.houghton@axleinfo.com), Najib Ishaq (najib.ishaq@nih.gov)",
@@ -8,7 +8,7 @@
   "repository": "https://github.com/polusai/image-tools",
   "website": "https://ncats.nih.gov/preclinical/core/informatics",
   "citation": "",
-  "containerId": "polusai/imagej-threshold-apply-tool:0.5.0",
+  "containerId": "polusai/imagej-threshold-apply-tool:0.5.1-dev0",
   "baseCommand": [
     "python3",
     "-m",
diff --git a/segmentation/imagej-threshold-apply-tool/pyproject.toml b/segmentation/imagej-threshold-apply-tool/pyproject.toml
index f3222d0af..d91bc7789 100644
--- a/segmentation/imagej-threshold-apply-tool/pyproject.toml
+++ b/segmentation/imagej-threshold-apply-tool/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "polus-images-segmentation-imagej-threshold-apply"
-version = "0.5.0"
+version = "0.5.1-dev0"
 description = ""
 authors = [
     "Nick Schaub <nick.schaub@nih.gov>",
diff --git a/segmentation/imagej-threshold-apply-tool/src/polus/images/segmentation/imagej_threshold_apply/__init__.py b/segmentation/imagej-threshold-apply-tool/src/polus/images/segmentation/imagej_threshold_apply/__init__.py
index d27db33c2..bc3e29434 100644
--- a/segmentation/imagej-threshold-apply-tool/src/polus/images/segmentation/imagej_threshold_apply/__init__.py
+++ b/segmentation/imagej-threshold-apply-tool/src/polus/images/segmentation/imagej_threshold_apply/__init__.py
@@ -1,7 +1,7 @@
 """Provides the ImageJ Threshold Apply tool."""
 
 
-__version__ = "0.5.0"
+__version__ = "0.5.1-dev0"
 
 
 import logging
diff --git a/segmentation/imagej-threshold-huang-tool/.bumpversion.cfg b/segmentation/imagej-threshold-huang-tool/.bumpversion.cfg
index 8b5937854..1ce4180d9 100644
--- a/segmentation/imagej-threshold-huang-tool/.bumpversion.cfg
+++ b/segmentation/imagej-threshold-huang-tool/.bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.5.0
+current_version = 0.5.1-dev0
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<dev>\d+))?
diff --git a/segmentation/imagej-threshold-huang-tool/Dockerfile b/segmentation/imagej-threshold-huang-tool/Dockerfile
index 45ca97115..316a4600c 100644
--- a/segmentation/imagej-threshold-huang-tool/Dockerfile
+++ b/segmentation/imagej-threshold-huang-tool/Dockerfile
@@ -24,5 +24,5 @@ RUN pip3 install "${EXEC_DIR}/image-tools/${TOOL_DIR}" --no-cache-dir
 
 # Set the entrypoint
 # TODO: Change the entrypoint to the tool entrypoint
-ENTRYPOINT ["python3", "-m", "polus.images.segmentation.imagej_threshold_hunag"]
+ENTRYPOINT ["python3", "-m", "polus.images.segmentation.imagej_threshold_huang"]
 CMD ["--help"]
diff --git a/segmentation/imagej-threshold-huang-tool/README.md b/segmentation/imagej-threshold-huang-tool/README.md
index c9328a9f9..610c5a43b 100644
--- a/segmentation/imagej-threshold-huang-tool/README.md
+++ b/segmentation/imagej-threshold-huang-tool/README.md
@@ -1,4 +1,4 @@
-# ImageJ threshold huang (v0.5.0)
+# ImageJ threshold huang (v0.5.1-dev0)
 
 This plugin implements Huang's threshold method proposed in Image Thresholding by Minimizing the Measures of Fuzziness, Huang (1995).
 This method determines an optimal thresholding value such that the fuzziness measure between the original image and its binary version is minimized.
diff --git a/segmentation/imagej-threshold-huang-tool/VERSION b/segmentation/imagej-threshold-huang-tool/VERSION
index 8f0916f76..6f9bb2cc0 100644
--- a/segmentation/imagej-threshold-huang-tool/VERSION
+++ b/segmentation/imagej-threshold-huang-tool/VERSION
@@ -1 +1 @@
-0.5.0
+0.5.1-dev0
diff --git a/segmentation/imagej-threshold-huang-tool/build-docker.sh b/segmentation/imagej-threshold-huang-tool/build-docker.sh
index 385291273..61c8655a9 100755
--- a/segmentation/imagej-threshold-huang-tool/build-docker.sh
+++ b/segmentation/imagej-threshold-huang-tool/build-docker.sh
@@ -1,3 +1,4 @@
+
 #!/bin/bash
 
 # Change the name of the tool here
diff --git a/segmentation/imagej-threshold-huang-tool/plugin.json b/segmentation/imagej-threshold-huang-tool/plugin.json
index 1df599b1d..d1ae89edb 100644
--- a/segmentation/imagej-threshold-huang-tool/plugin.json
+++ b/segmentation/imagej-threshold-huang-tool/plugin.json
@@ -1,6 +1,6 @@
 {
   "name": "ImageJ threshold huang",
-  "version": "0.5.0",
+  "version": "0.5.1-dev0",
   "title": "ImageJ threshold huang",
   "description": "This plugin implements Huang's threshold method by Huang Wang.",
   "author": "Nick Schaub (nick.schaub@nih.gov), Anjali Taneja, Benjamin Houghton (benjamin.houghton@axleinfo.com), Najib Ishaq (najib.ishaq@nih.gov)",
@@ -8,7 +8,7 @@
   "repository": "https://github.com/polusai/image-tools",
   "website": "https://ncats.nih.gov/preclinical/core/informatics",
   "citation": "",
-  "containerId": "polusai/imagej-threshold-huang-tool:0.5.0",
+  "containerId": "polusai/imagej-threshold-huang-tool:0.5.1-dev0",
   "inputs": [
     {
       "name": "inpDir",
diff --git a/segmentation/imagej-threshold-huang-tool/pyproject.toml b/segmentation/imagej-threshold-huang-tool/pyproject.toml
index c9e367eaf..52963e9d6 100644
--- a/segmentation/imagej-threshold-huang-tool/pyproject.toml
+++ b/segmentation/imagej-threshold-huang-tool/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "polus-images-segmentation-imagej-threshold-huang"
-version = "0.5.0"
+version = "0.5.1-dev0"
 description = ""
 authors = [
     "Nick Schaub <nick.schaub@nih.gov>",
diff --git a/segmentation/imagej-threshold-huang-tool/src/polus/images/segmentation/imagej_threshold_huang/__init__.py b/segmentation/imagej-threshold-huang-tool/src/polus/images/segmentation/imagej_threshold_huang/__init__.py
index 403f84916..b8fe93a5d 100644
--- a/segmentation/imagej-threshold-huang-tool/src/polus/images/segmentation/imagej_threshold_huang/__init__.py
+++ b/segmentation/imagej-threshold-huang-tool/src/polus/images/segmentation/imagej_threshold_huang/__init__.py
@@ -1,7 +1,7 @@
 """Provides the ImageJ Threshold Huang tool."""
 
 
-__version__ = "0.5.0"
+__version__ = "0.5.1-dev0"
 
 
 import logging
diff --git a/segmentation/imagej-threshold-ij1-tool/Dockerfile b/segmentation/imagej-threshold-ij1-tool/Dockerfile
index 1be31ef19..4230350d3 100644
--- a/segmentation/imagej-threshold-ij1-tool/Dockerfile
+++ b/segmentation/imagej-threshold-ij1-tool/Dockerfile
@@ -9,28 +9,20 @@ ENV POLUS_LOG="INFO"
 # Work directory defined in the base container
 WORKDIR ${EXEC_DIR}
 
-# ImageJ setup
+# Initialize ImageJ
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
-# Install the ImageJ Threshold Apply tool
-COPY imagej-threshold-apply-tool ${EXEC_DIR}/imagej-threshold-apply-tool
-RUN pip3 install ${EXEC_DIR}/imagej-threshold-apply-tool --no-cache-dir
+# TODO: Change the tool_dir to the tool directory
+ENV TOOL_DIR="segmentation/imagej-threshold-ij1-tool"
 
-RUN mkdir ${EXEC_DIR}/imagej-threshold-ij1-tool
-WORKDIR ${EXEC_DIR}/imagej-threshold-ij1-tool
+# Copy the repository into the container
+RUN mkdir image-tools
+COPY . ${EXEC_DIR}/image-tools
 
-# Install the python package
-COPY pyproject.toml .
-COPY VERSION .
-COPY README.md .
-COPY src ./src
-COPY tests ./tests
-
-RUN pip3 install ${EXEC_DIR}/imagej-threshold-ij1-tool --no-cache-dir
-
-RUN pip3 install scikit-image pytest pytest-sugar pytest-json-report --no-cache-dir
-RUN python3 -X faulthandler -m pytest --json-report --json-report-summary -v -p no:faulthandler
-RUN cat .report.json
+# Install the tool
+RUN pip3 install "${EXEC_DIR}/image-tools/${TOOL_DIR}" --no-cache-dir
 
+# Set the entrypoint
+# TODO: Change the entrypoint to the tool entrypoint
 ENTRYPOINT ["python3", "-m", "polus.images.segmentation.imagej_threshold_ij1"]
 CMD ["--help"]
diff --git a/segmentation/imagej-threshold-ij1-tool/build-docker.sh b/segmentation/imagej-threshold-ij1-tool/build-docker.sh
index a4e43fb55..d42022e99 100755
--- a/segmentation/imagej-threshold-ij1-tool/build-docker.sh
+++ b/segmentation/imagej-threshold-ij1-tool/build-docker.sh
@@ -1,8 +1,23 @@
+
 #!/bin/bash
 
-cp -r ../imagej-threshold-apply-tool .
+# Change the name of the tool here
+tool_dir="segmentation"
+tool_name="imagej-threshold-ij1-tool"
 
+# The version is read from the VERSION file
 version=$(<VERSION)
-docker build . -t polusai/imagej-threshold-ij1-tool:${version}
+tag="polusai/${tool_name}:${version}"
+echo "Building docker image with tag: ${tag}"
+
+# The current directory and the repository root are saved in variables
+cur_dir=$(pwd)
+repo_root=$(git rev-parse --show-toplevel)
 
-rm -rf imagej-threshold-apply-tool
+# The Dockerfile and .dockerignore files are copied to the repository root before building the image
+cd ${repo_root}
+cp ./${tool_dir}/${tool_name}/Dockerfile .
+cp .gitingore .dockerignore
+docker build . -t ${tag}
+rm Dockerfile .dockerignore
+cd ${cur_dir}
diff --git a/segmentation/imagej-threshold-intermodes-tool/Dockerfile b/segmentation/imagej-threshold-intermodes-tool/Dockerfile
index acf24e6ad..b939c673e 100644
--- a/segmentation/imagej-threshold-intermodes-tool/Dockerfile
+++ b/segmentation/imagej-threshold-intermodes-tool/Dockerfile
@@ -9,28 +9,20 @@ ENV POLUS_LOG="INFO"
 # Work directory defined in the base container
 WORKDIR ${EXEC_DIR}
 
-# ImageJ setup
+# Initialize ImageJ
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
-# Install the ImageJ Threshold Apply tool
-COPY imagej-threshold-apply-tool ${EXEC_DIR}/imagej-threshold-apply-tool
-RUN pip3 install ${EXEC_DIR}/imagej-threshold-apply-tool --no-cache-dir
+# TODO: Change the tool_dir to the tool directory
+ENV TOOL_DIR="segmentation/imagej-threshold-intermodes-tool"
 
-RUN mkdir ${EXEC_DIR}/imagej-threshold-intermodes-tool
-WORKDIR ${EXEC_DIR}/imagej-threshold-intermodes-tool
+# Copy the repository into the container
+RUN mkdir image-tools
+COPY . ${EXEC_DIR}/image-tools
 
-# Install the python package
-COPY pyproject.toml .
-COPY VERSION .
-COPY README.md .
-COPY src ./src
-COPY tests ./tests
-
-RUN pip3 install ${EXEC_DIR}/imagej-threshold-intermodes-tool --no-cache-dir
-
-RUN pip3 install scikit-image pytest pytest-sugar pytest-json-report --no-cache-dir
-RUN python3 -X faulthandler -m pytest --json-report --json-report-summary -v -p no:faulthandler
-RUN cat .report.json
+# Install the tool
+RUN pip3 install "${EXEC_DIR}/image-tools/${TOOL_DIR}" --no-cache-dir
 
+# Set the entrypoint
+# TODO: Change the entrypoint to the tool entrypoint
 ENTRYPOINT ["python3", "-m", "polus.images.segmentation.imagej_threshold_intermodes"]
 CMD ["--help"]
diff --git a/segmentation/imagej-threshold-intermodes-tool/build-docker.sh b/segmentation/imagej-threshold-intermodes-tool/build-docker.sh
index a7aee0617..3000e290f 100755
--- a/segmentation/imagej-threshold-intermodes-tool/build-docker.sh
+++ b/segmentation/imagej-threshold-intermodes-tool/build-docker.sh
@@ -1,8 +1,23 @@
+
 #!/bin/bash
 
-cp -r ../imagej-threshold-apply-tool .
+# Change the name of the tool here
+tool_dir="segmentation"
+tool_name="imagej-threshold-intermodes-tool"
 
+# The version is read from the VERSION file
 version=$(<VERSION)
-docker build . -t polusai/imagej-threshold-intermodes-tool:${version}
+tag="polusai/${tool_name}:${version}"
+echo "Building docker image with tag: ${tag}"
+
+# The current directory and the repository root are saved in variables
+cur_dir=$(pwd)
+repo_root=$(git rev-parse --show-toplevel)
 
-rm -rf imagej-threshold-apply-tool
+# The Dockerfile and .dockerignore files are copied to the repository root before building the image
+cd ${repo_root}
+cp ./${tool_dir}/${tool_name}/Dockerfile .
+cp .gitingore .dockerignore
+docker build . -t ${tag}
+rm Dockerfile .dockerignore
+cd ${cur_dir}
diff --git a/segmentation/imagej-threshold-isodata-tool/Dockerfile b/segmentation/imagej-threshold-isodata-tool/Dockerfile
index 5602cf82a..01cb6b90e 100644
--- a/segmentation/imagej-threshold-isodata-tool/Dockerfile
+++ b/segmentation/imagej-threshold-isodata-tool/Dockerfile
@@ -9,28 +9,20 @@ ENV POLUS_LOG="INFO"
 # Work directory defined in the base container
 WORKDIR ${EXEC_DIR}
 
-# ImageJ setup
+# Initialize ImageJ
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
-# Install the ImageJ Threshold Apply tool
-COPY imagej-threshold-apply-tool ${EXEC_DIR}/imagej-threshold-apply-tool
-RUN pip3 install ${EXEC_DIR}/imagej-threshold-apply-tool --no-cache-dir
+# TODO: Change the tool_dir to the tool directory
+ENV TOOL_DIR="segmentation/imagej-threshold-isodata-tool"
 
-RUN mkdir ${EXEC_DIR}/imagej-threshold-isodata-tool
-WORKDIR ${EXEC_DIR}/imagej-threshold-isodata-tool
+# Copy the repository into the container
+RUN mkdir image-tools
+COPY . ${EXEC_DIR}/image-tools
 
-# Install the python package
-COPY pyproject.toml .
-COPY VERSION .
-COPY README.md .
-COPY src ./src
-COPY tests ./tests
-
-RUN pip3 install ${EXEC_DIR}/imagej-threshold-isodata-tool --no-cache-dir
-
-RUN pip3 install scikit-image pytest pytest-sugar pytest-json-report --no-cache-dir
-RUN python3 -X faulthandler -m pytest --json-report --json-report-summary -v -p no:faulthandler
-RUN cat .report.json
+# Install the tool
+RUN pip3 install "${EXEC_DIR}/image-tools/${TOOL_DIR}" --no-cache-dir
 
+# Set the entrypoint
+# TODO: Change the entrypoint to the tool entrypoint
 ENTRYPOINT ["python3", "-m", "polus.images.segmentation.imagej_threshold_isodata"]
 CMD ["--help"]
diff --git a/segmentation/imagej-threshold-isodata-tool/build-docker.sh b/segmentation/imagej-threshold-isodata-tool/build-docker.sh
index 35bae7e14..2d44de4b9 100755
--- a/segmentation/imagej-threshold-isodata-tool/build-docker.sh
+++ b/segmentation/imagej-threshold-isodata-tool/build-docker.sh
@@ -1,8 +1,23 @@
+
 #!/bin/bash
 
-cp -r ../imagej-threshold-apply-tool .
+# Change the name of the tool here
+tool_dir="segmentation"
+tool_name="imagej-threshold-isodata-tool"
 
+# The version is read from the VERSION file
 version=$(<VERSION)
-docker build . -t polusai/imagej-threshold-isodata-tool:${version}
+tag="polusai/${tool_name}:${version}"
+echo "Building docker image with tag: ${tag}"
+
+# The current directory and the repository root are saved in variables
+cur_dir=$(pwd)
+repo_root=$(git rev-parse --show-toplevel)
 
-rm -rf imagej-threshold-apply-tool
+# The Dockerfile and .dockerignore files are copied to the repository root before building the image
+cd ${repo_root}
+cp ./${tool_dir}/${tool_name}/Dockerfile .
+cp .gitingore .dockerignore
+docker build . -t ${tag}
+rm Dockerfile .dockerignore
+cd ${cur_dir}
diff --git a/segmentation/imagej-threshold-li-tool/Dockerfile b/segmentation/imagej-threshold-li-tool/Dockerfile
index 15d347f4b..de0af8b04 100644
--- a/segmentation/imagej-threshold-li-tool/Dockerfile
+++ b/segmentation/imagej-threshold-li-tool/Dockerfile
@@ -9,28 +9,20 @@ ENV POLUS_LOG="INFO"
 # Work directory defined in the base container
 WORKDIR ${EXEC_DIR}
 
-# ImageJ setup
+# Initialize ImageJ
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
-# Install the ImageJ Threshold Apply tool
-COPY imagej-threshold-apply-tool ${EXEC_DIR}/imagej-threshold-apply-tool
-RUN pip3 install ${EXEC_DIR}/imagej-threshold-apply-tool --no-cache-dir
+# TODO: Change the tool_dir to the tool directory
+ENV TOOL_DIR="segmentation/imagej-threshold-li-tool"
 
-RUN mkdir ${EXEC_DIR}/imagej-threshold-li-tool
-WORKDIR ${EXEC_DIR}/imagej-threshold-li-tool
+# Copy the repository into the container
+RUN mkdir image-tools
+COPY . ${EXEC_DIR}/image-tools
 
-# Install the python package
-COPY pyproject.toml .
-COPY VERSION .
-COPY README.md .
-COPY src ./src
-COPY tests ./tests
-
-RUN pip3 install ${EXEC_DIR}/imagej-threshold-li-tool --no-cache-dir
-
-RUN pip3 install scikit-image pytest pytest-sugar pytest-json-report --no-cache-dir
-RUN python3 -X faulthandler -m pytest --json-report --json-report-summary -v -p no:faulthandler
-RUN cat .report.json
+# Install the tool
+RUN pip3 install "${EXEC_DIR}/image-tools/${TOOL_DIR}" --no-cache-dir
 
+# Set the entrypoint
+# TODO: Change the entrypoint to the tool entrypoint
 ENTRYPOINT ["python3", "-m", "polus.images.segmentation.imagej_threshold_li"]
 CMD ["--help"]
diff --git a/segmentation/imagej-threshold-li-tool/build-docker.sh b/segmentation/imagej-threshold-li-tool/build-docker.sh
index 334815cc1..f1b0ca62c 100755
--- a/segmentation/imagej-threshold-li-tool/build-docker.sh
+++ b/segmentation/imagej-threshold-li-tool/build-docker.sh
@@ -1,8 +1,23 @@
+
 #!/bin/bash
 
-cp -r ../imagej-threshold-apply-tool .
+# Change the name of the tool here
+tool_dir="segmentation"
+tool_name="imagej-threshold-li-tool"
 
+# The version is read from the VERSION file
 version=$(<VERSION)
-docker build . -t polusai/imagej-threshold-li-tool:${version}
+tag="polusai/${tool_name}:${version}"
+echo "Building docker image with tag: ${tag}"
+
+# The current directory and the repository root are saved in variables
+cur_dir=$(pwd)
+repo_root=$(git rev-parse --show-toplevel)
 
-rm -rf imagej-threshold-apply-tool
+# The Dockerfile and .dockerignore files are copied to the repository root before building the image
+cd ${repo_root}
+cp ./${tool_dir}/${tool_name}/Dockerfile .
+cp .gitingore .dockerignore
+docker build . -t ${tag}
+rm Dockerfile .dockerignore
+cd ${cur_dir}
diff --git a/segmentation/imagej-threshold-maxentropy-tool/Dockerfile b/segmentation/imagej-threshold-maxentropy-tool/Dockerfile
index 42744f694..9a4c48e87 100644
--- a/segmentation/imagej-threshold-maxentropy-tool/Dockerfile
+++ b/segmentation/imagej-threshold-maxentropy-tool/Dockerfile
@@ -9,28 +9,20 @@ ENV POLUS_LOG="INFO"
 # Work directory defined in the base container
 WORKDIR ${EXEC_DIR}
 
-# ImageJ setup
+# Initialize ImageJ
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
-# Install the ImageJ Threshold Apply tool
-COPY imagej-threshold-apply-tool ${EXEC_DIR}/imagej-threshold-apply-tool
-RUN pip3 install ${EXEC_DIR}/imagej-threshold-apply-tool --no-cache-dir
+# TODO: Change the tool_dir to the tool directory
+ENV TOOL_DIR="segmentation/imagej-threshold-maxentropy-tool"
 
-RUN mkdir ${EXEC_DIR}/imagej-threshold-maxentropy-tool
-WORKDIR ${EXEC_DIR}/imagej-threshold-maxentropy-tool
+# Copy the repository into the container
+RUN mkdir image-tools
+COPY . ${EXEC_DIR}/image-tools
 
-# Install the python package
-COPY pyproject.toml .
-COPY VERSION .
-COPY README.md .
-COPY src ./src
-COPY tests ./tests
-
-RUN pip3 install ${EXEC_DIR}/imagej-threshold-maxentropy-tool --no-cache-dir
-
-RUN pip3 install scikit-image pytest pytest-sugar pytest-json-report --no-cache-dir
-RUN python3 -X faulthandler -m pytest --json-report --json-report-summary -v -p no:faulthandler
-RUN cat .report.json
+# Install the tool
+RUN pip3 install "${EXEC_DIR}/image-tools/${TOOL_DIR}" --no-cache-dir
 
+# Set the entrypoint
+# TODO: Change the entrypoint to the tool entrypoint
 ENTRYPOINT ["python3", "-m", "polus.images.segmentation.imagej_threshold_maxentropy"]
 CMD ["--help"]
diff --git a/segmentation/imagej-threshold-maxentropy-tool/build-docker.sh b/segmentation/imagej-threshold-maxentropy-tool/build-docker.sh
index 29840114f..108225000 100755
--- a/segmentation/imagej-threshold-maxentropy-tool/build-docker.sh
+++ b/segmentation/imagej-threshold-maxentropy-tool/build-docker.sh
@@ -1,8 +1,23 @@
+
 #!/bin/bash
 
-cp -r ../imagej-threshold-apply-tool .
+# Change the name of the tool here
+tool_dir="segmentation"
+tool_name="imagej-threshold-maxentropy-tool"
 
+# The version is read from the VERSION file
 version=$(<VERSION)
-docker build . -t polusai/imagej-threshold-maxentropy-tool:${version}
+tag="polusai/${tool_name}:${version}"
+echo "Building docker image with tag: ${tag}"
+
+# The current directory and the repository root are saved in variables
+cur_dir=$(pwd)
+repo_root=$(git rev-parse --show-toplevel)
 
-rm -rf imagej-threshold-apply-tool
+# The Dockerfile and .dockerignore files are copied to the repository root before building the image
+cd ${repo_root}
+cp ./${tool_dir}/${tool_name}/Dockerfile .
+cp .gitingore .dockerignore
+docker build . -t ${tag}
+rm Dockerfile .dockerignore
+cd ${cur_dir}
diff --git a/segmentation/imagej-threshold-maxlikelihood-tool/Dockerfile b/segmentation/imagej-threshold-maxlikelihood-tool/Dockerfile
index 6d6cd4643..5132a0e12 100644
--- a/segmentation/imagej-threshold-maxlikelihood-tool/Dockerfile
+++ b/segmentation/imagej-threshold-maxlikelihood-tool/Dockerfile
@@ -9,28 +9,20 @@ ENV POLUS_LOG="INFO"
 # Work directory defined in the base container
 WORKDIR ${EXEC_DIR}
 
-# ImageJ setup
+# Initialize ImageJ
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
-# Install the ImageJ Threshold Apply tool
-COPY imagej-threshold-apply-tool ${EXEC_DIR}/imagej-threshold-apply-tool
-RUN pip3 install ${EXEC_DIR}/imagej-threshold-apply-tool --no-cache-dir
+# TODO: Change the tool_dir to the tool directory
+ENV TOOL_DIR="segmentation/imagej-threshold-maxlikelihood-tool"
 
-RUN mkdir ${EXEC_DIR}/imagej-threshold-maxlikelihood-tool
-WORKDIR ${EXEC_DIR}/imagej-threshold-maxlikelihood-tool
+# Copy the repository into the container
+RUN mkdir image-tools
+COPY . ${EXEC_DIR}/image-tools
 
-# Install the python package
-COPY pyproject.toml .
-COPY VERSION .
-COPY README.md .
-COPY src ./src
-COPY tests ./tests
-
-RUN pip3 install ${EXEC_DIR}/imagej-threshold-maxlikelihood-tool --no-cache-dir
-
-RUN pip3 install scikit-image pytest pytest-sugar pytest-json-report --no-cache-dir
-RUN python3 -X faulthandler -m pytest --json-report --json-report-summary -v -p no:faulthandler
-RUN cat .report.json
+# Install the tool
+RUN pip3 install "${EXEC_DIR}/image-tools/${TOOL_DIR}" --no-cache-dir
 
+# Set the entrypoint
+# TODO: Change the entrypoint to the tool entrypoint
 ENTRYPOINT ["python3", "-m", "polus.images.segmentation.imagej_threshold_maxlikelihood"]
 CMD ["--help"]
diff --git a/segmentation/imagej-threshold-maxlikelihood-tool/build-docker.sh b/segmentation/imagej-threshold-maxlikelihood-tool/build-docker.sh
index ccff5f6a1..da673dd6e 100755
--- a/segmentation/imagej-threshold-maxlikelihood-tool/build-docker.sh
+++ b/segmentation/imagej-threshold-maxlikelihood-tool/build-docker.sh
@@ -1,8 +1,23 @@
+
 #!/bin/bash
 
-cp -r ../imagej-threshold-apply-tool .
+# Change the name of the tool here
+tool_dir="segmentation"
+tool_name="imagej-threshold-maxlikelihood-tool"
 
+# The version is read from the VERSION file
 version=$(<VERSION)
-docker build . -t polusai/imagej-threshold-maxlikelihood-tool:${version}
+tag="polusai/${tool_name}:${version}"
+echo "Building docker image with tag: ${tag}"
+
+# The current directory and the repository root are saved in variables
+cur_dir=$(pwd)
+repo_root=$(git rev-parse --show-toplevel)
 
-rm -rf imagej-threshold-apply-tool
+# The Dockerfile and .dockerignore files are copied to the repository root before building the image
+cd ${repo_root}
+cp ./${tool_dir}/${tool_name}/Dockerfile .
+cp .gitingore .dockerignore
+docker build . -t ${tag}
+rm Dockerfile .dockerignore
+cd ${cur_dir}
diff --git a/segmentation/imagej-threshold-mean-tool/Dockerfile b/segmentation/imagej-threshold-mean-tool/Dockerfile
index 173118bd2..e0f041f45 100644
--- a/segmentation/imagej-threshold-mean-tool/Dockerfile
+++ b/segmentation/imagej-threshold-mean-tool/Dockerfile
@@ -9,28 +9,20 @@ ENV POLUS_LOG="INFO"
 # Work directory defined in the base container
 WORKDIR ${EXEC_DIR}
 
-# ImageJ setup
+# Initialize ImageJ
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
-# Install the ImageJ Threshold Apply tool
-COPY imagej-threshold-apply-tool ${EXEC_DIR}/imagej-threshold-apply-tool
-RUN pip3 install ${EXEC_DIR}/imagej-threshold-apply-tool --no-cache-dir
+# TODO: Change the tool_dir to the tool directory
+ENV TOOL_DIR="segmentation/imagej-threshold-mean-tool"
 
-RUN mkdir ${EXEC_DIR}/imagej-threshold-mean-tool
-WORKDIR ${EXEC_DIR}/imagej-threshold-mean-tool
+# Copy the repository into the container
+RUN mkdir image-tools
+COPY . ${EXEC_DIR}/image-tools
 
-# Install the python package
-COPY pyproject.toml .
-COPY VERSION .
-COPY README.md .
-COPY src ./src
-COPY tests ./tests
-
-RUN pip3 install ${EXEC_DIR}/imagej-threshold-mean-tool --no-cache-dir
-
-RUN pip3 install scikit-image pytest pytest-sugar pytest-json-report --no-cache-dir
-RUN python3 -X faulthandler -m pytest --json-report --json-report-summary -v -p no:faulthandler
-RUN cat .report.json
+# Install the tool
+RUN pip3 install "${EXEC_DIR}/image-tools/${TOOL_DIR}" --no-cache-dir
 
+# Set the entrypoint
+# TODO: Change the entrypoint to the tool entrypoint
 ENTRYPOINT ["python3", "-m", "polus.images.segmentation.imagej_threshold_mean"]
 CMD ["--help"]
diff --git a/segmentation/imagej-threshold-mean-tool/build-docker.sh b/segmentation/imagej-threshold-mean-tool/build-docker.sh
index b1ef08273..78d55ec17 100755
--- a/segmentation/imagej-threshold-mean-tool/build-docker.sh
+++ b/segmentation/imagej-threshold-mean-tool/build-docker.sh
@@ -1,8 +1,23 @@
+
 #!/bin/bash
 
-cp -r ../imagej-threshold-apply-tool .
+# Change the name of the tool here
+tool_dir="segmentation"
+tool_name="imagej-threshold-mean-tool"
 
+# The version is read from the VERSION file
 version=$(<VERSION)
-docker build . -t polusai/imagej-threshold-mean-tool:${version}
+tag="polusai/${tool_name}:${version}"
+echo "Building docker image with tag: ${tag}"
+
+# The current directory and the repository root are saved in variables
+cur_dir=$(pwd)
+repo_root=$(git rev-parse --show-toplevel)
 
-rm -rf imagej-threshold-apply-tool
+# The Dockerfile and .dockerignore files are copied to the repository root before building the image
+cd ${repo_root}
+cp ./${tool_dir}/${tool_name}/Dockerfile .
+cp .gitingore .dockerignore
+docker build . -t ${tag}
+rm Dockerfile .dockerignore
+cd ${cur_dir}
diff --git a/segmentation/imagej-threshold-minerror-tool/Dockerfile b/segmentation/imagej-threshold-minerror-tool/Dockerfile
index a7c464747..f8f7ca87f 100644
--- a/segmentation/imagej-threshold-minerror-tool/Dockerfile
+++ b/segmentation/imagej-threshold-minerror-tool/Dockerfile
@@ -9,28 +9,20 @@ ENV POLUS_LOG="INFO"
 # Work directory defined in the base container
 WORKDIR ${EXEC_DIR}
 
-# ImageJ setup
+# Initialize ImageJ
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
-# Install the ImageJ Threshold Apply tool
-COPY imagej-threshold-apply-tool ${EXEC_DIR}/imagej-threshold-apply-tool
-RUN pip3 install ${EXEC_DIR}/imagej-threshold-apply-tool --no-cache-dir
+# TODO: Change the tool_dir to the tool directory
+ENV TOOL_DIR="segmentation/imagej-threshold-minerror-tool"
 
-RUN mkdir ${EXEC_DIR}/imagej-threshold-minerror-tool
-WORKDIR ${EXEC_DIR}/imagej-threshold-minerror-tool
+# Copy the repository into the container
+RUN mkdir image-tools
+COPY . ${EXEC_DIR}/image-tools
 
-# Install the python package
-COPY pyproject.toml .
-COPY VERSION .
-COPY README.md .
-COPY src ./src
-COPY tests ./tests
-
-RUN pip3 install ${EXEC_DIR}/imagej-threshold-minerror-tool --no-cache-dir
-
-RUN pip3 install scikit-image pytest pytest-sugar pytest-json-report --no-cache-dir
-RUN python3 -X faulthandler -m pytest --json-report --json-report-summary -v -p no:faulthandler
-RUN cat .report.json
+# Install the tool
+RUN pip3 install "${EXEC_DIR}/image-tools/${TOOL_DIR}" --no-cache-dir
 
+# Set the entrypoint
+# TODO: Change the entrypoint to the tool entrypoint
 ENTRYPOINT ["python3", "-m", "polus.images.segmentation.imagej_threshold_minerror"]
 CMD ["--help"]
diff --git a/segmentation/imagej-threshold-minerror-tool/build-docker.sh b/segmentation/imagej-threshold-minerror-tool/build-docker.sh
index 27f981b77..e450e79ff 100755
--- a/segmentation/imagej-threshold-minerror-tool/build-docker.sh
+++ b/segmentation/imagej-threshold-minerror-tool/build-docker.sh
@@ -1,8 +1,23 @@
+
 #!/bin/bash
 
-cp -r ../imagej-threshold-apply-tool .
+# Change the name of the tool here
+tool_dir="segmentation"
+tool_name="imagej-threshold-minerror-tool"
 
+# The version is read from the VERSION file
 version=$(<VERSION)
-docker build . -t polusai/imagej-threshold-minerror-tool:${version}
+tag="polusai/${tool_name}:${version}"
+echo "Building docker image with tag: ${tag}"
+
+# The current directory and the repository root are saved in variables
+cur_dir=$(pwd)
+repo_root=$(git rev-parse --show-toplevel)
 
-rm -rf imagej-threshold-apply-tool
+# The Dockerfile and .dockerignore files are copied to the repository root before building the image
+cd ${repo_root}
+cp ./${tool_dir}/${tool_name}/Dockerfile .
+cp .gitingore .dockerignore
+docker build . -t ${tag}
+rm Dockerfile .dockerignore
+cd ${cur_dir}
diff --git a/segmentation/imagej-threshold-minimum-tool/Dockerfile b/segmentation/imagej-threshold-minimum-tool/Dockerfile
index 59db01eaa..35df52981 100644
--- a/segmentation/imagej-threshold-minimum-tool/Dockerfile
+++ b/segmentation/imagej-threshold-minimum-tool/Dockerfile
@@ -9,28 +9,20 @@ ENV POLUS_LOG="INFO"
 # Work directory defined in the base container
 WORKDIR ${EXEC_DIR}
 
-# ImageJ setup
+# Initialize ImageJ
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
-# Install the ImageJ Threshold Apply tool
-COPY imagej-threshold-apply-tool ${EXEC_DIR}/imagej-threshold-apply-tool
-RUN pip3 install ${EXEC_DIR}/imagej-threshold-apply-tool --no-cache-dir
+# TODO: Change the tool_dir to the tool directory
+ENV TOOL_DIR="segmentation/imagej-threshold-minimum-tool"
 
-RUN mkdir ${EXEC_DIR}/imagej-threshold-minimum-tool
-WORKDIR ${EXEC_DIR}/imagej-threshold-minimum-tool
+# Copy the repository into the container
+RUN mkdir image-tools
+COPY . ${EXEC_DIR}/image-tools
 
-# Install the python package
-COPY pyproject.toml .
-COPY VERSION .
-COPY README.md .
-COPY src ./src
-COPY tests ./tests
-
-RUN pip3 install ${EXEC_DIR}/imagej-threshold-minimum-tool --no-cache-dir
-
-RUN pip3 install scikit-image pytest pytest-sugar pytest-json-report --no-cache-dir
-RUN python3 -X faulthandler -m pytest --json-report --json-report-summary -v -p no:faulthandler
-RUN cat .report.json
+# Install the tool
+RUN pip3 install "${EXEC_DIR}/image-tools/${TOOL_DIR}" --no-cache-dir
 
+# Set the entrypoint
+# TODO: Change the entrypoint to the tool entrypoint
 ENTRYPOINT ["python3", "-m", "polus.images.segmentation.imagej_threshold_minimum"]
 CMD ["--help"]
diff --git a/segmentation/imagej-threshold-minimum-tool/build-docker.sh b/segmentation/imagej-threshold-minimum-tool/build-docker.sh
index 84338bc81..140c7b85d 100755
--- a/segmentation/imagej-threshold-minimum-tool/build-docker.sh
+++ b/segmentation/imagej-threshold-minimum-tool/build-docker.sh
@@ -1,8 +1,23 @@
+
 #!/bin/bash
 
-cp -r ../imagej-threshold-apply-tool .
+# Change the name of the tool here
+tool_dir="segmentation"
+tool_name="imagej-threshold-minimum-tool"
 
+# The version is read from the VERSION file
 version=$(<VERSION)
-docker build . -t polusai/imagej-threshold-minimum-tool:${version}
+tag="polusai/${tool_name}:${version}"
+echo "Building docker image with tag: ${tag}"
+
+# The current directory and the repository root are saved in variables
+cur_dir=$(pwd)
+repo_root=$(git rev-parse --show-toplevel)
 
-rm -rf imagej-threshold-apply-tool
+# The Dockerfile and .dockerignore files are copied to the repository root before building the image
+cd ${repo_root}
+cp ./${tool_dir}/${tool_name}/Dockerfile .
+cp .gitingore .dockerignore
+docker build . -t ${tag}
+rm Dockerfile .dockerignore
+cd ${cur_dir}
diff --git a/segmentation/imagej-threshold-moments-tool/Dockerfile b/segmentation/imagej-threshold-moments-tool/Dockerfile
index c206ee55c..757887ec3 100644
--- a/segmentation/imagej-threshold-moments-tool/Dockerfile
+++ b/segmentation/imagej-threshold-moments-tool/Dockerfile
@@ -9,28 +9,20 @@ ENV POLUS_LOG="INFO"
 # Work directory defined in the base container
 WORKDIR ${EXEC_DIR}
 
-# ImageJ setup
+# Initialize ImageJ
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
-# Install the ImageJ Threshold Apply tool
-COPY imagej-threshold-apply-tool ${EXEC_DIR}/imagej-threshold-apply-tool
-RUN pip3 install ${EXEC_DIR}/imagej-threshold-apply-tool --no-cache-dir
+# TODO: Change the tool_dir to the tool directory
+ENV TOOL_DIR="segmentation/imagej-threshold-moments-tool"
 
-RUN mkdir ${EXEC_DIR}/imagej-threshold-moments-tool
-WORKDIR ${EXEC_DIR}/imagej-threshold-moments-tool
+# Copy the repository into the container
+RUN mkdir image-tools
+COPY . ${EXEC_DIR}/image-tools
 
-# Install the python package
-COPY pyproject.toml .
-COPY VERSION .
-COPY README.md .
-COPY src ./src
-COPY tests ./tests
-
-RUN pip3 install ${EXEC_DIR}/imagej-threshold-moments-tool --no-cache-dir
-
-RUN pip3 install scikit-image pytest pytest-sugar pytest-json-report --no-cache-dir
-RUN python3 -X faulthandler -m pytest --json-report --json-report-summary -v -p no:faulthandler
-RUN cat .report.json
+# Install the tool
+RUN pip3 install "${EXEC_DIR}/image-tools/${TOOL_DIR}" --no-cache-dir
 
+# Set the entrypoint
+# TODO: Change the entrypoint to the tool entrypoint
 ENTRYPOINT ["python3", "-m", "polus.images.segmentation.imagej_threshold_moments"]
 CMD ["--help"]
diff --git a/segmentation/imagej-threshold-moments-tool/build-docker.sh b/segmentation/imagej-threshold-moments-tool/build-docker.sh
index d06159a5f..93907eb74 100755
--- a/segmentation/imagej-threshold-moments-tool/build-docker.sh
+++ b/segmentation/imagej-threshold-moments-tool/build-docker.sh
@@ -1,8 +1,23 @@
+
 #!/bin/bash
 
-cp -r ../imagej-threshold-apply-tool .
+# Change the name of the tool here
+tool_dir="segmentation"
+tool_name="imagej-threshold-moments-tool"
 
+# The version is read from the VERSION file
 version=$(<VERSION)
-docker build . -t polusai/imagej-threshold-moments-tool:${version}
+tag="polusai/${tool_name}:${version}"
+echo "Building docker image with tag: ${tag}"
+
+# The current directory and the repository root are saved in variables
+cur_dir=$(pwd)
+repo_root=$(git rev-parse --show-toplevel)
 
-rm -rf imagej-threshold-apply-tool
+# The Dockerfile and .dockerignore files are copied to the repository root before building the image
+cd ${repo_root}
+cp ./${tool_dir}/${tool_name}/Dockerfile .
+cp .gitingore .dockerignore
+docker build . -t ${tag}
+rm Dockerfile .dockerignore
+cd ${cur_dir}
diff --git a/segmentation/imagej-threshold-otsu-tool/Dockerfile b/segmentation/imagej-threshold-otsu-tool/Dockerfile
index e39077990..0357799c0 100644
--- a/segmentation/imagej-threshold-otsu-tool/Dockerfile
+++ b/segmentation/imagej-threshold-otsu-tool/Dockerfile
@@ -9,28 +9,20 @@ ENV POLUS_LOG="INFO"
 # Work directory defined in the base container
 WORKDIR ${EXEC_DIR}
 
-# ImageJ setup
+# Initialize ImageJ
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
-# Install the ImageJ Threshold Apply tool
-COPY imagej-threshold-apply-tool ${EXEC_DIR}/imagej-threshold-apply-tool
-RUN pip3 install ${EXEC_DIR}/imagej-threshold-apply-tool --no-cache-dir
+# TODO: Change the tool_dir to the tool directory
+ENV TOOL_DIR="segmentation/imagej-threshold-otsu-tool"
 
-RUN mkdir ${EXEC_DIR}/imagej-threshold-otsu-tool
-WORKDIR ${EXEC_DIR}/imagej-threshold-otsu-tool
+# Copy the repository into the container
+RUN mkdir image-tools
+COPY . ${EXEC_DIR}/image-tools
 
-# Install the python package
-COPY pyproject.toml .
-COPY VERSION .
-COPY README.md .
-COPY src ./src
-COPY tests ./tests
-
-RUN pip3 install ${EXEC_DIR}/imagej-threshold-otsu-tool --no-cache-dir
-
-RUN pip3 install scikit-image pytest pytest-sugar pytest-json-report --no-cache-dir
-RUN python3 -X faulthandler -m pytest --json-report --json-report-summary -v -p no:faulthandler
-RUN cat .report.json
+# Install the tool
+RUN pip3 install "${EXEC_DIR}/image-tools/${TOOL_DIR}" --no-cache-dir
 
+# Set the entrypoint
+# TODO: Change the entrypoint to the tool entrypoint
 ENTRYPOINT ["python3", "-m", "polus.images.segmentation.imagej_threshold_otsu"]
 CMD ["--help"]
diff --git a/segmentation/imagej-threshold-otsu-tool/build-docker.sh b/segmentation/imagej-threshold-otsu-tool/build-docker.sh
index 98ba90f75..b800b7855 100755
--- a/segmentation/imagej-threshold-otsu-tool/build-docker.sh
+++ b/segmentation/imagej-threshold-otsu-tool/build-docker.sh
@@ -1,8 +1,23 @@
+
 #!/bin/bash
 
-cp -r ../imagej-threshold-apply-tool .
+# Change the name of the tool here
+tool_dir="segmentation"
+tool_name="imagej-threshold-otsu-tool"
 
+# The version is read from the VERSION file
 version=$(<VERSION)
-docker build . -t polusai/imagej-threshold-otsu-tool:${version}
+tag="polusai/${tool_name}:${version}"
+echo "Building docker image with tag: ${tag}"
+
+# The current directory and the repository root are saved in variables
+cur_dir=$(pwd)
+repo_root=$(git rev-parse --show-toplevel)
 
-rm -rf imagej-threshold-apply-tool
+# The Dockerfile and .dockerignore files are copied to the repository root before building the image
+cd ${repo_root}
+cp ./${tool_dir}/${tool_name}/Dockerfile .
+cp .gitingore .dockerignore
+docker build . -t ${tag}
+rm Dockerfile .dockerignore
+cd ${cur_dir}
diff --git a/segmentation/imagej-threshold-percentile-tool/Dockerfile b/segmentation/imagej-threshold-percentile-tool/Dockerfile
index 30d04fd71..dcd6c8588 100644
--- a/segmentation/imagej-threshold-percentile-tool/Dockerfile
+++ b/segmentation/imagej-threshold-percentile-tool/Dockerfile
@@ -9,28 +9,20 @@ ENV POLUS_LOG="INFO"
 # Work directory defined in the base container
 WORKDIR ${EXEC_DIR}
 
-# ImageJ setup
+# Initialize ImageJ
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
-# Install the ImageJ Threshold Apply tool
-COPY imagej-threshold-apply-tool ${EXEC_DIR}/imagej-threshold-apply-tool
-RUN pip3 install ${EXEC_DIR}/imagej-threshold-apply-tool --no-cache-dir
+# TODO: Change the tool_dir to the tool directory
+ENV TOOL_DIR="segmentation/imagej-threshold-percentile-tool"
 
-RUN mkdir ${EXEC_DIR}/imagej-threshold-percentile-tool
-WORKDIR ${EXEC_DIR}/imagej-threshold-percentile-tool
+# Copy the repository into the container
+RUN mkdir image-tools
+COPY . ${EXEC_DIR}/image-tools
 
-# Install the python package
-COPY pyproject.toml .
-COPY VERSION .
-COPY README.md .
-COPY src ./src
-COPY tests ./tests
-
-RUN pip3 install ${EXEC_DIR}/imagej-threshold-percentile-tool --no-cache-dir
-
-RUN pip3 install scikit-image pytest pytest-sugar pytest-json-report --no-cache-dir
-RUN python3 -X faulthandler -m pytest --json-report --json-report-summary -v -p no:faulthandler
-RUN cat .report.json
+# Install the tool
+RUN pip3 install "${EXEC_DIR}/image-tools/${TOOL_DIR}" --no-cache-dir
 
+# Set the entrypoint
+# TODO: Change the entrypoint to the tool entrypoint
 ENTRYPOINT ["python3", "-m", "polus.images.segmentation.imagej_threshold_percentile"]
 CMD ["--help"]
diff --git a/segmentation/imagej-threshold-percentile-tool/build-docker.sh b/segmentation/imagej-threshold-percentile-tool/build-docker.sh
index d9a30b4b1..31d8712ef 100755
--- a/segmentation/imagej-threshold-percentile-tool/build-docker.sh
+++ b/segmentation/imagej-threshold-percentile-tool/build-docker.sh
@@ -1,8 +1,23 @@
+
 #!/bin/bash
 
-cp -r ../imagej-threshold-apply-tool .
+# Change the name of the tool here
+tool_dir="segmentation"
+tool_name="imagej-threshold-percentile-tool"
 
+# The version is read from the VERSION file
 version=$(<VERSION)
-docker build . -t polusai/imagej-threshold-percentile-tool:${version}
+tag="polusai/${tool_name}:${version}"
+echo "Building docker image with tag: ${tag}"
+
+# The current directory and the repository root are saved in variables
+cur_dir=$(pwd)
+repo_root=$(git rev-parse --show-toplevel)
 
-rm -rf imagej-threshold-apply-tool
+# The Dockerfile and .dockerignore files are copied to the repository root before building the image
+cd ${repo_root}
+cp ./${tool_dir}/${tool_name}/Dockerfile .
+cp .gitingore .dockerignore
+docker build . -t ${tag}
+rm Dockerfile .dockerignore
+cd ${cur_dir}
diff --git a/segmentation/imagej-threshold-renyientropy-tool/Dockerfile b/segmentation/imagej-threshold-renyientropy-tool/Dockerfile
index 1a984e9db..8b45683df 100644
--- a/segmentation/imagej-threshold-renyientropy-tool/Dockerfile
+++ b/segmentation/imagej-threshold-renyientropy-tool/Dockerfile
@@ -9,28 +9,20 @@ ENV POLUS_LOG="INFO"
 # Work directory defined in the base container
 WORKDIR ${EXEC_DIR}
 
-# ImageJ setup
+# Initialize ImageJ
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
-# Install the ImageJ Threshold Apply tool
-COPY imagej-threshold-apply-tool ${EXEC_DIR}/imagej-threshold-apply-tool
-RUN pip3 install ${EXEC_DIR}/imagej-threshold-apply-tool --no-cache-dir
+# TODO: Change the tool_dir to the tool directory
+ENV TOOL_DIR="segmentation/imagej-threshold-renyientropy-tool"
 
-RUN mkdir ${EXEC_DIR}/imagej-threshold-renyientropy-tool
-WORKDIR ${EXEC_DIR}/imagej-threshold-renyientropy-tool
+# Copy the repository into the container
+RUN mkdir image-tools
+COPY . ${EXEC_DIR}/image-tools
 
-# Install the python package
-COPY pyproject.toml .
-COPY VERSION .
-COPY README.md .
-COPY src ./src
-COPY tests ./tests
-
-RUN pip3 install ${EXEC_DIR}/imagej-threshold-renyientropy-tool --no-cache-dir
-
-RUN pip3 install scikit-image pytest pytest-sugar pytest-json-report --no-cache-dir
-RUN python3 -X faulthandler -m pytest --json-report --json-report-summary -v -p no:faulthandler
-RUN cat .report.json
+# Install the tool
+RUN pip3 install "${EXEC_DIR}/image-tools/${TOOL_DIR}" --no-cache-dir
 
+# Set the entrypoint
+# TODO: Change the entrypoint to the tool entrypoint
 ENTRYPOINT ["python3", "-m", "polus.images.segmentation.imagej_threshold_renyientropy"]
 CMD ["--help"]
diff --git a/segmentation/imagej-threshold-renyientropy-tool/build-docker.sh b/segmentation/imagej-threshold-renyientropy-tool/build-docker.sh
index 7e79c7473..bbdd90ced 100755
--- a/segmentation/imagej-threshold-renyientropy-tool/build-docker.sh
+++ b/segmentation/imagej-threshold-renyientropy-tool/build-docker.sh
@@ -1,8 +1,23 @@
+
 #!/bin/bash
 
-cp -r ../imagej-threshold-apply-tool .
+# Change the name of the tool here
+tool_dir="segmentation"
+tool_name="imagej-threshold-renyientropy-tool"
 
+# The version is read from the VERSION file
 version=$(<VERSION)
-docker build . -t polusai/imagej-threshold-renyientropy-tool:${version}
+tag="polusai/${tool_name}:${version}"
+echo "Building docker image with tag: ${tag}"
+
+# The current directory and the repository root are saved in variables
+cur_dir=$(pwd)
+repo_root=$(git rev-parse --show-toplevel)
 
-rm -rf imagej-threshold-apply-tool
+# The Dockerfile and .dockerignore files are copied to the repository root before building the image
+cd ${repo_root}
+cp ./${tool_dir}/${tool_name}/Dockerfile .
+cp .gitingore .dockerignore
+docker build . -t ${tag}
+rm Dockerfile .dockerignore
+cd ${cur_dir}
diff --git a/segmentation/imagej-threshold-rosin-tool/Dockerfile b/segmentation/imagej-threshold-rosin-tool/Dockerfile
index 77fc22b2f..1336b7d0b 100644
--- a/segmentation/imagej-threshold-rosin-tool/Dockerfile
+++ b/segmentation/imagej-threshold-rosin-tool/Dockerfile
@@ -9,28 +9,20 @@ ENV POLUS_LOG="INFO"
 # Work directory defined in the base container
 WORKDIR ${EXEC_DIR}
 
-# ImageJ setup
+# Initialize ImageJ
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
-# Install the ImageJ Threshold Apply tool
-COPY imagej-threshold-apply-tool ${EXEC_DIR}/imagej-threshold-apply-tool
-RUN pip3 install ${EXEC_DIR}/imagej-threshold-apply-tool --no-cache-dir
+# TODO: Change the tool_dir to the tool directory
+ENV TOOL_DIR="segmentation/imagej-threshold-rosin-tool"
 
-RUN mkdir ${EXEC_DIR}/imagej-threshold-rosin-tool
-WORKDIR ${EXEC_DIR}/imagej-threshold-rosin-tool
+# Copy the repository into the container
+RUN mkdir image-tools
+COPY . ${EXEC_DIR}/image-tools
 
-# Install the python package
-COPY pyproject.toml .
-COPY VERSION .
-COPY README.md .
-COPY src ./src
-COPY tests ./tests
-
-RUN pip3 install ${EXEC_DIR}/imagej-threshold-rosin-tool --no-cache-dir
-
-RUN pip3 install scikit-image pytest pytest-sugar pytest-json-report --no-cache-dir
-RUN python3 -X faulthandler -m pytest --json-report --json-report-summary -v -p no:faulthandler
-RUN cat .report.json
+# Install the tool
+RUN pip3 install "${EXEC_DIR}/image-tools/${TOOL_DIR}" --no-cache-dir
 
+# Set the entrypoint
+# TODO: Change the entrypoint to the tool entrypoint
 ENTRYPOINT ["python3", "-m", "polus.images.segmentation.imagej_threshold_rosin"]
 CMD ["--help"]
diff --git a/segmentation/imagej-threshold-rosin-tool/build-docker.sh b/segmentation/imagej-threshold-rosin-tool/build-docker.sh
index d8b3674fb..edc178009 100755
--- a/segmentation/imagej-threshold-rosin-tool/build-docker.sh
+++ b/segmentation/imagej-threshold-rosin-tool/build-docker.sh
@@ -1,8 +1,23 @@
+
 #!/bin/bash
 
-cp -r ../imagej-threshold-apply-tool .
+# Change the name of the tool here
+tool_dir="segmentation"
+tool_name="imagej-threshold-rosin-tool"
 
+# The version is read from the VERSION file
 version=$(<VERSION)
-docker build . -t polusai/imagej-threshold-rosin-tool:${version}
+tag="polusai/${tool_name}:${version}"
+echo "Building docker image with tag: ${tag}"
+
+# The current directory and the repository root are saved in variables
+cur_dir=$(pwd)
+repo_root=$(git rev-parse --show-toplevel)
 
-rm -rf imagej-threshold-apply-tool
+# The Dockerfile and .dockerignore files are copied to the repository root before building the image
+cd ${repo_root}
+cp ./${tool_dir}/${tool_name}/Dockerfile .
+cp .gitingore .dockerignore
+docker build . -t ${tag}
+rm Dockerfile .dockerignore
+cd ${cur_dir}
diff --git a/segmentation/imagej-threshold-shanbhag-tool/Dockerfile b/segmentation/imagej-threshold-shanbhag-tool/Dockerfile
index cd81d76c8..a0834ba07 100644
--- a/segmentation/imagej-threshold-shanbhag-tool/Dockerfile
+++ b/segmentation/imagej-threshold-shanbhag-tool/Dockerfile
@@ -9,28 +9,20 @@ ENV POLUS_LOG="INFO"
 # Work directory defined in the base container
 WORKDIR ${EXEC_DIR}
 
-# ImageJ setup
+# Initialize ImageJ
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
-# Install the ImageJ Threshold Apply tool
-COPY imagej-threshold-apply-tool ${EXEC_DIR}/imagej-threshold-apply-tool
-RUN pip3 install ${EXEC_DIR}/imagej-threshold-apply-tool --no-cache-dir
+# TODO: Change the tool_dir to the tool directory
+ENV TOOL_DIR="segmentation/imagej-threshold-shanbhag-tool"
 
-RUN mkdir ${EXEC_DIR}/imagej-threshold-shanbhag-tool
-WORKDIR ${EXEC_DIR}/imagej-threshold-shanbhag-tool
+# Copy the repository into the container
+RUN mkdir image-tools
+COPY . ${EXEC_DIR}/image-tools
 
-# Install the python package
-COPY pyproject.toml .
-COPY VERSION .
-COPY README.md .
-COPY src ./src
-COPY tests ./tests
-
-RUN pip3 install ${EXEC_DIR}/imagej-threshold-shanbhag-tool --no-cache-dir
-
-RUN pip3 install scikit-image pytest pytest-sugar pytest-json-report --no-cache-dir
-RUN python3 -X faulthandler -m pytest --json-report --json-report-summary -v -p no:faulthandler
-RUN cat .report.json
+# Install the tool
+RUN pip3 install "${EXEC_DIR}/image-tools/${TOOL_DIR}" --no-cache-dir
 
+# Set the entrypoint
+# TODO: Change the entrypoint to the tool entrypoint
 ENTRYPOINT ["python3", "-m", "polus.images.segmentation.imagej_threshold_shanbhag"]
 CMD ["--help"]
diff --git a/segmentation/imagej-threshold-shanbhag-tool/build-docker.sh b/segmentation/imagej-threshold-shanbhag-tool/build-docker.sh
index c4b3f8958..f18adeb88 100755
--- a/segmentation/imagej-threshold-shanbhag-tool/build-docker.sh
+++ b/segmentation/imagej-threshold-shanbhag-tool/build-docker.sh
@@ -1,8 +1,23 @@
+
 #!/bin/bash
 
-cp -r ../imagej-threshold-apply-tool .
+# Change the name of the tool here
+tool_dir="segmentation"
+tool_name="imagej-threshold-shanbhag-tool"
 
+# The version is read from the VERSION file
 version=$(<VERSION)
-docker build . -t polusai/imagej-threshold-shanbhag-tool:${version}
+tag="polusai/${tool_name}:${version}"
+echo "Building docker image with tag: ${tag}"
+
+# The current directory and the repository root are saved in variables
+cur_dir=$(pwd)
+repo_root=$(git rev-parse --show-toplevel)
 
-rm -rf imagej-threshold-apply-tool
+# The Dockerfile and .dockerignore files are copied to the repository root before building the image
+cd ${repo_root}
+cp ./${tool_dir}/${tool_name}/Dockerfile .
+cp .gitingore .dockerignore
+docker build . -t ${tag}
+rm Dockerfile .dockerignore
+cd ${cur_dir}
diff --git a/segmentation/imagej-threshold-triangle-tool/Dockerfile b/segmentation/imagej-threshold-triangle-tool/Dockerfile
index c0854c890..abde199f7 100644
--- a/segmentation/imagej-threshold-triangle-tool/Dockerfile
+++ b/segmentation/imagej-threshold-triangle-tool/Dockerfile
@@ -9,28 +9,20 @@ ENV POLUS_LOG="INFO"
 # Work directory defined in the base container
 WORKDIR ${EXEC_DIR}
 
-# ImageJ setup
+# Initialize ImageJ
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
-# Install the ImageJ Threshold Apply tool
-COPY imagej-threshold-apply-tool ${EXEC_DIR}/imagej-threshold-apply-tool
-RUN pip3 install ${EXEC_DIR}/imagej-threshold-apply-tool --no-cache-dir
+# TODO: Change the tool_dir to the tool directory
+ENV TOOL_DIR="segmentation/imagej-threshold-triangle-tool"
 
-RUN mkdir ${EXEC_DIR}/imagej-threshold-triangle-tool
-WORKDIR ${EXEC_DIR}/imagej-threshold-triangle-tool
+# Copy the repository into the container
+RUN mkdir image-tools
+COPY . ${EXEC_DIR}/image-tools
 
-# Install the python package
-COPY pyproject.toml .
-COPY VERSION .
-COPY README.md .
-COPY src ./src
-COPY tests ./tests
-
-RUN pip3 install ${EXEC_DIR}/imagej-threshold-triangle-tool --no-cache-dir
-
-RUN pip3 install scikit-image pytest pytest-sugar pytest-json-report --no-cache-dir
-RUN python3 -X faulthandler -m pytest --json-report --json-report-summary -v -p no:faulthandler
-RUN cat .report.json
+# Install the tool
+RUN pip3 install "${EXEC_DIR}/image-tools/${TOOL_DIR}" --no-cache-dir
 
+# Set the entrypoint
+# TODO: Change the entrypoint to the tool entrypoint
 ENTRYPOINT ["python3", "-m", "polus.images.segmentation.imagej_threshold_triangle"]
 CMD ["--help"]
diff --git a/segmentation/imagej-threshold-triangle-tool/build-docker.sh b/segmentation/imagej-threshold-triangle-tool/build-docker.sh
index 43da57250..8fdc8e10a 100755
--- a/segmentation/imagej-threshold-triangle-tool/build-docker.sh
+++ b/segmentation/imagej-threshold-triangle-tool/build-docker.sh
@@ -1,8 +1,23 @@
+
 #!/bin/bash
 
-cp -r ../imagej-threshold-apply-tool .
+# Change the name of the tool here
+tool_dir="segmentation"
+tool_name="imagej-threshold-triangle-tool"
 
+# The version is read from the VERSION file
 version=$(<VERSION)
-docker build . -t polusai/imagej-threshold-triangle-tool:${version}
+tag="polusai/${tool_name}:${version}"
+echo "Building docker image with tag: ${tag}"
+
+# The current directory and the repository root are saved in variables
+cur_dir=$(pwd)
+repo_root=$(git rev-parse --show-toplevel)
 
-rm -rf imagej-threshold-apply-tool
+# The Dockerfile and .dockerignore files are copied to the repository root before building the image
+cd ${repo_root}
+cp ./${tool_dir}/${tool_name}/Dockerfile .
+cp .gitingore .dockerignore
+docker build . -t ${tag}
+rm Dockerfile .dockerignore
+cd ${cur_dir}
diff --git a/segmentation/imagej-threshold-yen-tool/Dockerfile b/segmentation/imagej-threshold-yen-tool/Dockerfile
index a13152204..2c0f59a7d 100644
--- a/segmentation/imagej-threshold-yen-tool/Dockerfile
+++ b/segmentation/imagej-threshold-yen-tool/Dockerfile
@@ -9,28 +9,20 @@ ENV POLUS_LOG="INFO"
 # Work directory defined in the base container
 WORKDIR ${EXEC_DIR}
 
-# ImageJ setup
+# Initialize ImageJ
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
-# Install the ImageJ Threshold Apply tool
-COPY imagej-threshold-apply-tool ${EXEC_DIR}/imagej-threshold-apply-tool
-RUN pip3 install ${EXEC_DIR}/imagej-threshold-apply-tool --no-cache-dir
+# TODO: Change the tool_dir to the tool directory
+ENV TOOL_DIR="segmentation/imagej-threshold-yen-tool"
 
-RUN mkdir ${EXEC_DIR}/imagej-threshold-yen-tool
-WORKDIR ${EXEC_DIR}/imagej-threshold-yen-tool
+# Copy the repository into the container
+RUN mkdir image-tools
+COPY . ${EXEC_DIR}/image-tools
 
-# Install the python package
-COPY pyproject.toml .
-COPY VERSION .
-COPY README.md .
-COPY src ./src
-COPY tests ./tests
-
-RUN pip3 install ${EXEC_DIR}/imagej-threshold-yen-tool --no-cache-dir
-
-RUN pip3 install scikit-image pytest pytest-sugar pytest-json-report --no-cache-dir
-RUN python3 -X faulthandler -m pytest --json-report --json-report-summary -v -p no:faulthandler
-RUN cat .report.json
+# Install the tool
+RUN pip3 install "${EXEC_DIR}/image-tools/${TOOL_DIR}" --no-cache-dir
 
+# Set the entrypoint
+# TODO: Change the entrypoint to the tool entrypoint
 ENTRYPOINT ["python3", "-m", "polus.images.segmentation.imagej_threshold_yen"]
 CMD ["--help"]
diff --git a/segmentation/imagej-threshold-yen-tool/build-docker.sh b/segmentation/imagej-threshold-yen-tool/build-docker.sh
index 00a462d8d..38bcf88fc 100755
--- a/segmentation/imagej-threshold-yen-tool/build-docker.sh
+++ b/segmentation/imagej-threshold-yen-tool/build-docker.sh
@@ -1,8 +1,23 @@
+
 #!/bin/bash
 
-cp -r ../imagej-threshold-apply-tool .
+# Change the name of the tool here
+tool_dir="segmentation"
+tool_name="imagej-threshold-yen-tool"
 
+# The version is read from the VERSION file
 version=$(<VERSION)
-docker build . -t polusai/imagej-threshold-yen-tool:${version}
+tag="polusai/${tool_name}:${version}"
+echo "Building docker image with tag: ${tag}"
+
+# The current directory and the repository root are saved in variables
+cur_dir=$(pwd)
+repo_root=$(git rev-parse --show-toplevel)
 
-rm -rf imagej-threshold-apply-tool
+# The Dockerfile and .dockerignore files are copied to the repository root before building the image
+cd ${repo_root}
+cp ./${tool_dir}/${tool_name}/Dockerfile .
+cp .gitingore .dockerignore
+docker build . -t ${tag}
+rm Dockerfile .dockerignore
+cd ${cur_dir}
diff --git a/segmentation/mesmer-inference-tool/Dockerfile b/segmentation/mesmer-inference-tool/Dockerfile
index d58828934..98ecf589b 100644
--- a/segmentation/mesmer-inference-tool/Dockerfile
+++ b/segmentation/mesmer-inference-tool/Dockerfile
@@ -1,35 +1,41 @@
-# Get Linux
 FROM nvidia/cuda:11.2.2-cudnn8-runtime-ubuntu20.04
 
 # environment variables defined in polusai/bfio
 ENV EXEC_DIR="/opt/executables"
 ENV POLUS_IMG_EXT=".ome.tif"
 ENV POLUS_TAB_EXT=".csv"
-
-# Container log level
 ENV POLUS_LOG="INFO"
+ENV TF_FORCE_GPU_ALLOW_GROWTH=true
 
-WORKDIR ${EXEC_DIR}
-COPY pyproject.toml ${EXEC_DIR}
-COPY VERSION ${EXEC_DIR}
-COPY README.md ${EXEC_DIR}
 
 # Instal Python
 RUN apt update && \
-    apt install software-properties-common -y && \
-    add-apt-repository ppa:deadsnakes/ppa && \
-    apt install python3.9 python3.9-dev python3.9-distutils curl openjdk-8-jre build-essential -y && \
-    curl https://bootstrap.pypa.io/get-pip.py -o get-pip.py && \
-    python3.9 get-pip.py && \
-    apt autoremove -y && \
-    rm -rf /var/lib/apt/lists/*
+apt install software-properties-common -y && \
+add-apt-repository ppa:deadsnakes/ppa && \
+apt install python3.9 python3.9-dev python3.9-distutils curl openjdk-8-jre build-essential -y && \
+curl https://bootstrap.pypa.io/get-pip.py -o get-pip.py && \
+python3.9 get-pip.py && \
+apt autoremove -y && \
+rm -rf /var/lib/apt/lists/*
 
 RUN ln -sf /usr/bin/python3.9 /usr/bin/python3
-RUN pip install --index-url https://test.pypi.org/simple/ filepattern==2.2.7
-COPY src ${EXEC_DIR}/src
-RUN pip3 install ${EXEC_DIR} --no-cache-dir
+
+WORKDIR ${EXEC_DIR}
+
+# TODO: Change the tool_dir to the tool directory
+ENV TOOL_DIR="segmentation/mesmer-inference-tool"
+
+# Copy the repository into the container
+RUN mkdir image-tools
+COPY . ${EXEC_DIR}/image-tools
+
+# Install the tool
+RUN pip3 install "${EXEC_DIR}/image-tools/${TOOL_DIR}" --no-cache-dir
+
 # Fix for cudnn error on RTX gpus
-ENV TF_FORCE_GPU_ALLOW_GROWTH=true
 RUN python3 -c "import deepcell;from deepcell.applications import Mesmer; app = Mesmer()"
+
+# Set the entrypoint
+# TODO: Change the entrypoint to the tool entrypoint
 ENTRYPOINT ["python3", "-m", "polus.images.segmentation.mesmer_inference"]
 CMD ["--help"]
diff --git a/segmentation/mesmer-inference-tool/build-docker.sh b/segmentation/mesmer-inference-tool/build-docker.sh
index ebb46630f..ea2906172 100644
--- a/segmentation/mesmer-inference-tool/build-docker.sh
+++ b/segmentation/mesmer-inference-tool/build-docker.sh
@@ -1,3 +1,23 @@
+
 #!/bin/bash
+
+# Change the name of the tool here
+tool_dir="segmentation"
+tool_name="mesmer-inference-tool"
+
+# The version is read from the VERSION file
 version=$(<VERSION)
-docker build . -t polusai/mesmer-inference-tool:${version}
+tag="polusai/${tool_name}:${version}"
+echo "Building docker image with tag: ${tag}"
+
+# The current directory and the repository root are saved in variables
+cur_dir=$(pwd)
+repo_root=$(git rev-parse --show-toplevel)
+
+# The Dockerfile and .dockerignore files are copied to the repository root before building the image
+cd ${repo_root}
+cp ./${tool_dir}/${tool_name}/Dockerfile .
+cp .gitingore .dockerignore
+docker build . -t ${tag}
+rm Dockerfile .dockerignore
+cd ${cur_dir}
diff --git a/segmentation/mesmer-training-tool/Dockerfile b/segmentation/mesmer-training-tool/Dockerfile
index 713942067..f0dfc1c89 100644
--- a/segmentation/mesmer-training-tool/Dockerfile
+++ b/segmentation/mesmer-training-tool/Dockerfile
@@ -1,34 +1,41 @@
-# Get Linux
 FROM nvidia/cuda:11.2.2-cudnn8-runtime-ubuntu20.04
 
 # environment variables defined in polusai/bfio
 ENV EXEC_DIR="/opt/executables"
 ENV POLUS_IMG_EXT=".ome.tif"
 ENV POLUS_TAB_EXT=".csv"
-
-# Container log level
 ENV POLUS_LOG="INFO"
+ENV TF_FORCE_GPU_ALLOW_GROWTH=true
 
-WORKDIR ${EXEC_DIR}
-COPY pyproject.toml ${EXEC_DIR}
-COPY VERSION ${EXEC_DIR}
-COPY README.md ${EXEC_DIR}
 
 # Instal Python
 RUN apt update && \
-    apt install software-properties-common -y && \
-    add-apt-repository ppa:deadsnakes/ppa && \
-    apt install python3.9 python3.9-dev python3.9-distutils curl openjdk-8-jre build-essential -y && \
-    curl https://bootstrap.pypa.io/get-pip.py -o get-pip.py && \
-    python3.9 get-pip.py && \
-    apt autoremove -y && \
-    rm -rf /var/lib/apt/lists/*
+apt install software-properties-common -y && \
+add-apt-repository ppa:deadsnakes/ppa && \
+apt install python3.9 python3.9-dev python3.9-distutils curl openjdk-8-jre build-essential -y && \
+curl https://bootstrap.pypa.io/get-pip.py -o get-pip.py && \
+python3.9 get-pip.py && \
+apt autoremove -y && \
+rm -rf /var/lib/apt/lists/*
 
 RUN ln -sf /usr/bin/python3.9 /usr/bin/python3
-RUN pip install --index-url https://test.pypi.org/simple/ filepattern==2.2.8
-COPY src ${EXEC_DIR}/src
-RUN pip3 install ${EXEC_DIR} --no-cache-dir
+
+WORKDIR ${EXEC_DIR}
+
+# TODO: Change the tool_dir to the tool directory
+ENV TOOL_DIR="segmentation/mesmer-training-tool"
+
+# Copy the repository into the container
+RUN mkdir image-tools
+COPY . ${EXEC_DIR}/image-tools
+
+# Install the tool
+RUN pip3 install "${EXEC_DIR}/image-tools/${TOOL_DIR}" --no-cache-dir
+
 # Fix for cudnn error on RTX gpus
-ENV TF_FORCE_GPU_ALLOW_GROWTH=true
+RUN python3 -c "import deepcell;from deepcell.applications import Mesmer; app = Mesmer()"
+
+# Set the entrypoint
+# TODO: Change the entrypoint to the tool entrypoint
 ENTRYPOINT ["python3", "-m", "polus.images.segmentation.mesmer_training"]
 CMD ["--help"]
diff --git a/segmentation/mesmer-training-tool/build-docker.sh b/segmentation/mesmer-training-tool/build-docker.sh
index a84e45e29..9dd39bf8e 100644
--- a/segmentation/mesmer-training-tool/build-docker.sh
+++ b/segmentation/mesmer-training-tool/build-docker.sh
@@ -1,3 +1,23 @@
+
 #!/bin/bash
+
+# Change the name of the tool here
+tool_dir="segmentation"
+tool_name="mesmer-training-tool"
+
+# The version is read from the VERSION file
 version=$(<VERSION)
-docker build . -t polusai/mesmer-training-tool:${version}
+tag="polusai/${tool_name}:${version}"
+echo "Building docker image with tag: ${tag}"
+
+# The current directory and the repository root are saved in variables
+cur_dir=$(pwd)
+repo_root=$(git rev-parse --show-toplevel)
+
+# The Dockerfile and .dockerignore files are copied to the repository root before building the image
+cd ${repo_root}
+cp ./${tool_dir}/${tool_name}/Dockerfile .
+cp .gitingore .dockerignore
+docker build . -t ${tag}
+rm Dockerfile .dockerignore
+cd ${cur_dir}
diff --git a/transforms/imagej-deconvolve-richardsonlucy-tool/Dockerfile b/transforms/imagej-deconvolve-richardsonlucy-tool/Dockerfile
index af6e6d1a3..e2051411f 100644
--- a/transforms/imagej-deconvolve-richardsonlucy-tool/Dockerfile
+++ b/transforms/imagej-deconvolve-richardsonlucy-tool/Dockerfile
@@ -9,29 +9,20 @@ ENV POLUS_LOG="INFO"
 # Work directory defined in the base container
 WORKDIR ${EXEC_DIR}
 
-# ImageJ setup
+# Initialize ImageJ
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
-# Install the ImageJ Threshold Apply tool
-COPY segmentation ${EXEC_DIR}/segmentation
-RUN pip3 install ${EXEC_DIR}/segmentation/imagej-threshold-apply-tool --no-cache-dir
+# TODO: Change the tool_dir to the tool directory
+ENV TOOL_DIR="transforms/imagej-deconvolve-richardsonlucy-tool"
 
-RUN mkdir ${EXEC_DIR}/transforms
-RUN mkdir ${EXEC_DIR}/transforms/imagej-deconvolve-richardsonlucy-tool
-WORKDIR ${EXEC_DIR}/transforms/imagej-deconvolve-richardsonlucy-tool
+# Copy the repository into the container
+RUN mkdir image-tools
+COPY . ${EXEC_DIR}/image-tools
 
-# Install the python package
-COPY pyproject.toml .
-COPY VERSION .
-COPY README.md .
-COPY src ./src
-COPY tests ./tests
-
-RUN pip3 install ${EXEC_DIR}/transforms/imagej-deconvolve-richardsonlucy-tool --no-cache-dir
-
-RUN pip3 install scikit-image scipy pytest pytest-sugar pytest-json-report --no-cache-dir
-RUN python3 -X faulthandler -m pytest --json-report --json-report-summary -v -p no:faulthandler
-RUN cat .report.json
+# Install the tool
+RUN pip3 install "${EXEC_DIR}/image-tools/${TOOL_DIR}" --no-cache-dir
 
+# Set the entrypoint
+# TODO: Change the entrypoint to the tool entrypoint
 ENTRYPOINT ["python3", "-m", "polus.images.transforms.imagej_deconvolve_richardsonlucy"]
 CMD ["--help"]
diff --git a/transforms/imagej-deconvolve-richardsonlucy-tool/build-docker.sh b/transforms/imagej-deconvolve-richardsonlucy-tool/build-docker.sh
index b1c069977..60022ca27 100755
--- a/transforms/imagej-deconvolve-richardsonlucy-tool/build-docker.sh
+++ b/transforms/imagej-deconvolve-richardsonlucy-tool/build-docker.sh
@@ -1,9 +1,23 @@
+
 #!/bin/bash
 
-mkdir segmentation
-cp -r ../../segmentation/imagej-threshold-apply-tool ./segmentation/.
+# Change the name of the tool here
+tool_dir="transforms"
+tool_name="imagej-deconvolve-richardsonlucy-tool"
 
+# The version is read from the VERSION file
 version=$(<VERSION)
-docker build . -t polusai/imagej-deconvolve-richardsonlucy-tool:${version}
+tag="polusai/${tool_name}:${version}"
+echo "Building docker image with tag: ${tag}"
+
+# The current directory and the repository root are saved in variables
+cur_dir=$(pwd)
+repo_root=$(git rev-parse --show-toplevel)
 
-rm -rf ./segmentation
+# The Dockerfile and .dockerignore files are copied to the repository root before building the image
+cd ${repo_root}
+cp ./${tool_dir}/${tool_name}/Dockerfile .
+cp .gitingore .dockerignore
+docker build . -t ${tag}
+rm Dockerfile .dockerignore
+cd ${cur_dir}
diff --git a/transforms/imagej-deconvolve-richardsonlucytv-tool/Dockerfile b/transforms/imagej-deconvolve-richardsonlucytv-tool/Dockerfile
index efab66035..cb38b0d8b 100644
--- a/transforms/imagej-deconvolve-richardsonlucytv-tool/Dockerfile
+++ b/transforms/imagej-deconvolve-richardsonlucytv-tool/Dockerfile
@@ -9,29 +9,20 @@ ENV POLUS_LOG="INFO"
 # Work directory defined in the base container
 WORKDIR ${EXEC_DIR}
 
-# ImageJ setup
+# Initialize ImageJ
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
-# Install the ImageJ Threshold Apply tool
-COPY segmentation ${EXEC_DIR}/segmentation
-RUN pip3 install ${EXEC_DIR}/segmentation/imagej-threshold-apply-tool --no-cache-dir
+# TODO: Change the tool_dir to the tool directory
+ENV TOOL_DIR="transforms/imagej-deconvolve-richardsonlucytv-tool"
 
-RUN mkdir ${EXEC_DIR}/transforms
-RUN mkdir ${EXEC_DIR}/transforms/imagej-deconvolve-richardsonlucytv-tool
-WORKDIR ${EXEC_DIR}/transforms/imagej-deconvolve-richardsonlucytv-tool
+# Copy the repository into the container
+RUN mkdir image-tools
+COPY . ${EXEC_DIR}/image-tools
 
-# Install the python package
-COPY pyproject.toml .
-COPY VERSION .
-COPY README.md .
-COPY src ./src
-COPY tests ./tests
-
-RUN pip3 install ${EXEC_DIR}/transforms/imagej-deconvolve-richardsonlucytv-tool --no-cache-dir
-
-RUN pip3 install scikit-image scipy pytest pytest-sugar pytest-json-report --no-cache-dir
-RUN python3 -X faulthandler -m pytest --json-report --json-report-summary -v -p no:faulthandler
-RUN cat .report.json
+# Install the tool
+RUN pip3 install "${EXEC_DIR}/image-tools/${TOOL_DIR}" --no-cache-dir
 
+# Set the entrypoint
+# TODO: Change the entrypoint to the tool entrypoint
 ENTRYPOINT ["python3", "-m", "polus.images.transforms.imagej_deconvolve_richardsonlucytv"]
 CMD ["--help"]
diff --git a/transforms/imagej-deconvolve-richardsonlucytv-tool/build-docker.sh b/transforms/imagej-deconvolve-richardsonlucytv-tool/build-docker.sh
index c3956d4f1..25c2fb4d8 100755
--- a/transforms/imagej-deconvolve-richardsonlucytv-tool/build-docker.sh
+++ b/transforms/imagej-deconvolve-richardsonlucytv-tool/build-docker.sh
@@ -1,9 +1,23 @@
+
 #!/bin/bash
 
-mkdir segmentation
-cp -r ../../segmentation/imagej-threshold-apply-tool ./segmentation/.
+# Change the name of the tool here
+tool_dir="transforms"
+tool_name="imagej-deconvolve-richardsonlucytv-tool"
 
+# The version is read from the VERSION file
 version=$(<VERSION)
-docker build . -t polusai/imagej-deconvolve-richardsonlucytv-tool:${version}
+tag="polusai/${tool_name}:${version}"
+echo "Building docker image with tag: ${tag}"
+
+# The current directory and the repository root are saved in variables
+cur_dir=$(pwd)
+repo_root=$(git rev-parse --show-toplevel)
 
-rm -rf ./segmentation
+# The Dockerfile and .dockerignore files are copied to the repository root before building the image
+cd ${repo_root}
+cp ./${tool_dir}/${tool_name}/Dockerfile .
+cp .gitingore .dockerignore
+docker build . -t ${tag}
+rm Dockerfile .dockerignore
+cd ${cur_dir}
diff --git a/transforms/imagej-filter-addpoissonnoise-tool/Dockerfile b/transforms/imagej-filter-addpoissonnoise-tool/Dockerfile
index 4f9bb4c25..07e99b948 100644
--- a/transforms/imagej-filter-addpoissonnoise-tool/Dockerfile
+++ b/transforms/imagej-filter-addpoissonnoise-tool/Dockerfile
@@ -9,29 +9,20 @@ ENV POLUS_LOG="INFO"
 # Work directory defined in the base container
 WORKDIR ${EXEC_DIR}
 
-# ImageJ setup
+# Initialize ImageJ
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
-# Install the ImageJ Threshold Apply tool
-COPY segmentation ${EXEC_DIR}/segmentation
-RUN pip3 install ${EXEC_DIR}/segmentation/imagej-threshold-apply-tool --no-cache-dir
+# TODO: Change the tool_dir to the tool directory
+ENV TOOL_DIR="transforms/imagej-filter-addpoissonnoise-tool"
 
-RUN mkdir ${EXEC_DIR}/transforms
-RUN mkdir ${EXEC_DIR}/transforms/imagej-filter-addpoissonnoise-tool
-WORKDIR ${EXEC_DIR}/transforms/imagej-filter-addpoissonnoise-tool
+# Copy the repository into the container
+RUN mkdir image-tools
+COPY . ${EXEC_DIR}/image-tools
 
-# Install the python package
-COPY pyproject.toml .
-COPY VERSION .
-COPY README.md .
-COPY src ./src
-COPY tests ./tests
-
-RUN pip3 install ${EXEC_DIR}/transforms/imagej-filter-addpoissonnoise-tool --no-cache-dir
-
-RUN pip3 install scikit-image scipy pytest pytest-sugar pytest-json-report --no-cache-dir
-RUN python3 -X faulthandler -m pytest --json-report --json-report-summary -v -p no:faulthandler
-RUN cat .report.json
+# Install the tool
+RUN pip3 install "${EXEC_DIR}/image-tools/${TOOL_DIR}" --no-cache-dir
 
+# Set the entrypoint
+# TODO: Change the entrypoint to the tool entrypoint
 ENTRYPOINT ["python3", "-m", "polus.images.transforms.imagej_filter_addpoissonnoise"]
 CMD ["--help"]
diff --git a/transforms/imagej-filter-addpoissonnoise-tool/build-docker.sh b/transforms/imagej-filter-addpoissonnoise-tool/build-docker.sh
index 2d5ec980e..ec3a3c81c 100755
--- a/transforms/imagej-filter-addpoissonnoise-tool/build-docker.sh
+++ b/transforms/imagej-filter-addpoissonnoise-tool/build-docker.sh
@@ -1,9 +1,23 @@
+
 #!/bin/bash
 
-mkdir segmentation
-cp -r ../../segmentation/imagej-threshold-apply-tool ./segmentation/.
+# Change the name of the tool here
+tool_dir="transforms"
+tool_name="imagej-filter-addpoissonnoise-tool"
 
+# The version is read from the VERSION file
 version=$(<VERSION)
-docker build . -t polusai/imagej-filter-addpoissonnoise-tool:${version}
+tag="polusai/${tool_name}:${version}"
+echo "Building docker image with tag: ${tag}"
+
+# The current directory and the repository root are saved in variables
+cur_dir=$(pwd)
+repo_root=$(git rev-parse --show-toplevel)
 
-rm -rf ./segmentation
+# The Dockerfile and .dockerignore files are copied to the repository root before building the image
+cd ${repo_root}
+cp ./${tool_dir}/${tool_name}/Dockerfile .
+cp .gitingore .dockerignore
+docker build . -t ${tag}
+rm Dockerfile .dockerignore
+cd ${cur_dir}
diff --git a/transforms/imagej-filter-convolve-tool/Dockerfile b/transforms/imagej-filter-convolve-tool/Dockerfile
index 527e538c5..7e7b65f8b 100644
--- a/transforms/imagej-filter-convolve-tool/Dockerfile
+++ b/transforms/imagej-filter-convolve-tool/Dockerfile
@@ -9,29 +9,20 @@ ENV POLUS_LOG="INFO"
 # Work directory defined in the base container
 WORKDIR ${EXEC_DIR}
 
-# ImageJ setup
+# Initialize ImageJ
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
-# Install the ImageJ Threshold Apply tool
-COPY segmentation ${EXEC_DIR}/segmentation
-RUN pip3 install ${EXEC_DIR}/segmentation/imagej-threshold-apply-tool --no-cache-dir
+# TODO: Change the tool_dir to the tool directory
+ENV TOOL_DIR="transforms/imagej-filter-convolve-tool"
 
-RUN mkdir ${EXEC_DIR}/transforms
-RUN mkdir ${EXEC_DIR}/transforms/imagej-filter-convolve-tool
-WORKDIR ${EXEC_DIR}/transforms/imagej-filter-convolve-tool
+# Copy the repository into the container
+RUN mkdir image-tools
+COPY . ${EXEC_DIR}/image-tools
 
-# Install the python package
-COPY pyproject.toml .
-COPY VERSION .
-COPY README.md .
-COPY src ./src
-COPY tests ./tests
-
-RUN pip3 install ${EXEC_DIR}/transforms/imagej-filter-convolve-tool --no-cache-dir
-
-RUN pip3 install scikit-image scipy pytest pytest-sugar pytest-json-report --no-cache-dir
-RUN python3 -X faulthandler -m pytest --json-report --json-report-summary -v -p no:faulthandler
-RUN cat .report.json
+# Install the tool
+RUN pip3 install "${EXEC_DIR}/image-tools/${TOOL_DIR}" --no-cache-dir
 
+# Set the entrypoint
+# TODO: Change the entrypoint to the tool entrypoint
 ENTRYPOINT ["python3", "-m", "polus.images.transforms.imagej_filter_convolve"]
 CMD ["--help"]
diff --git a/transforms/imagej-filter-convolve-tool/build-docker.sh b/transforms/imagej-filter-convolve-tool/build-docker.sh
index e6aa1f386..e01be0d36 100755
--- a/transforms/imagej-filter-convolve-tool/build-docker.sh
+++ b/transforms/imagej-filter-convolve-tool/build-docker.sh
@@ -1,9 +1,23 @@
+
 #!/bin/bash
 
-mkdir segmentation
-cp -r ../../segmentation/imagej-threshold-apply-tool ./segmentation/.
+# Change the name of the tool here
+tool_dir="transforms"
+tool_name="imagej-filter-convolve-tool"
 
+# The version is read from the VERSION file
 version=$(<VERSION)
-docker build . -t polusai/imagej-filter-convolve-tool:${version}
+tag="polusai/${tool_name}:${version}"
+echo "Building docker image with tag: ${tag}"
+
+# The current directory and the repository root are saved in variables
+cur_dir=$(pwd)
+repo_root=$(git rev-parse --show-toplevel)
 
-rm -rf ./segmentation
+# The Dockerfile and .dockerignore files are copied to the repository root before building the image
+cd ${repo_root}
+cp ./${tool_dir}/${tool_name}/Dockerfile .
+cp .gitingore .dockerignore
+docker build . -t ${tag}
+rm Dockerfile .dockerignore
+cd ${cur_dir}
diff --git a/transforms/imagej-filter-correlate-tool/Dockerfile b/transforms/imagej-filter-correlate-tool/Dockerfile
index bf90eb87a..7fe63bfae 100644
--- a/transforms/imagej-filter-correlate-tool/Dockerfile
+++ b/transforms/imagej-filter-correlate-tool/Dockerfile
@@ -9,29 +9,20 @@ ENV POLUS_LOG="INFO"
 # Work directory defined in the base container
 WORKDIR ${EXEC_DIR}
 
-# ImageJ setup
+# Initialize ImageJ
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
-# Install the ImageJ Threshold Apply tool
-COPY segmentation ${EXEC_DIR}/segmentation
-RUN pip3 install ${EXEC_DIR}/segmentation/imagej-threshold-apply-tool --no-cache-dir
+# TODO: Change the tool_dir to the tool directory
+ENV TOOL_DIR="transforms/imagej-filter-correlate-tool"
 
-RUN mkdir ${EXEC_DIR}/transforms
-RUN mkdir ${EXEC_DIR}/transforms/imagej-filter-correlate-tool
-WORKDIR ${EXEC_DIR}/transforms/imagej-filter-correlate-tool
+# Copy the repository into the container
+RUN mkdir image-tools
+COPY . ${EXEC_DIR}/image-tools
 
-# Install the python package
-COPY pyproject.toml .
-COPY VERSION .
-COPY README.md .
-COPY src ./src
-COPY tests ./tests
-
-RUN pip3 install ${EXEC_DIR}/transforms/imagej-filter-correlate-tool --no-cache-dir
-
-RUN pip3 install scikit-image scipy pytest pytest-sugar pytest-json-report --no-cache-dir
-RUN python3 -X faulthandler -m pytest --json-report --json-report-summary -v -p no:faulthandler
-RUN cat .report.json
+# Install the tool
+RUN pip3 install "${EXEC_DIR}/image-tools/${TOOL_DIR}" --no-cache-dir
 
+# Set the entrypoint
+# TODO: Change the entrypoint to the tool entrypoint
 ENTRYPOINT ["python3", "-m", "polus.images.transforms.imagej_filter_correlate"]
 CMD ["--help"]
diff --git a/transforms/imagej-filter-correlate-tool/build-docker.sh b/transforms/imagej-filter-correlate-tool/build-docker.sh
index f09cd6ab9..b286be857 100755
--- a/transforms/imagej-filter-correlate-tool/build-docker.sh
+++ b/transforms/imagej-filter-correlate-tool/build-docker.sh
@@ -1,9 +1,23 @@
+
 #!/bin/bash
 
-mkdir segmentation
-cp -r ../../segmentation/imagej-threshold-apply-tool ./segmentation/.
+# Change the name of the tool here
+tool_dir="transforms"
+tool_name="imagej-filter-correlate-tool"
 
+# The version is read from the VERSION file
 version=$(<VERSION)
-docker build . -t polusai/imagej-filter-correlate-tool:${version}
+tag="polusai/${tool_name}:${version}"
+echo "Building docker image with tag: ${tag}"
+
+# The current directory and the repository root are saved in variables
+cur_dir=$(pwd)
+repo_root=$(git rev-parse --show-toplevel)
 
-rm -rf ./segmentation
+# The Dockerfile and .dockerignore files are copied to the repository root before building the image
+cd ${repo_root}
+cp ./${tool_dir}/${tool_name}/Dockerfile .
+cp .gitingore .dockerignore
+docker build . -t ${tag}
+rm Dockerfile .dockerignore
+cd ${cur_dir}
diff --git a/transforms/imagej-filter-derivativegauss-tool/Dockerfile b/transforms/imagej-filter-derivativegauss-tool/Dockerfile
index 27639ef1c..137cafd7a 100644
--- a/transforms/imagej-filter-derivativegauss-tool/Dockerfile
+++ b/transforms/imagej-filter-derivativegauss-tool/Dockerfile
@@ -9,29 +9,20 @@ ENV POLUS_LOG="INFO"
 # Work directory defined in the base container
 WORKDIR ${EXEC_DIR}
 
-# ImageJ setup
+# Initialize ImageJ
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
-# Install the ImageJ Threshold Apply tool
-COPY segmentation ${EXEC_DIR}/segmentation
-RUN pip3 install ${EXEC_DIR}/segmentation/imagej-threshold-apply-tool --no-cache-dir
+# TODO: Change the tool_dir to the tool directory
+ENV TOOL_DIR="transforms/imagej-filter-derivativegauss-tool"
 
-RUN mkdir ${EXEC_DIR}/transforms
-RUN mkdir ${EXEC_DIR}/transforms/imagej-filter-derivativegauss-tool
-WORKDIR ${EXEC_DIR}/transforms/imagej-filter-derivativegauss-tool
+# Copy the repository into the container
+RUN mkdir image-tools
+COPY . ${EXEC_DIR}/image-tools
 
-# Install the python package
-COPY pyproject.toml .
-COPY VERSION .
-COPY README.md .
-COPY src ./src
-COPY tests ./tests
-
-RUN pip3 install ${EXEC_DIR}/transforms/imagej-filter-derivativegauss-tool --no-cache-dir
-
-RUN pip3 install scikit-image scipy pytest pytest-sugar pytest-json-report --no-cache-dir
-RUN python3 -X faulthandler -m pytest --json-report --json-report-summary -v -p no:faulthandler
-RUN cat .report.json
+# Install the tool
+RUN pip3 install "${EXEC_DIR}/image-tools/${TOOL_DIR}" --no-cache-dir
 
+# Set the entrypoint
+# TODO: Change the entrypoint to the tool entrypoint
 ENTRYPOINT ["python3", "-m", "polus.images.transforms.imagej_filter_derivativegauss"]
 CMD ["--help"]
diff --git a/transforms/imagej-filter-derivativegauss-tool/build-docker.sh b/transforms/imagej-filter-derivativegauss-tool/build-docker.sh
index dc8f9f8ee..5c7e1db84 100755
--- a/transforms/imagej-filter-derivativegauss-tool/build-docker.sh
+++ b/transforms/imagej-filter-derivativegauss-tool/build-docker.sh
@@ -1,9 +1,23 @@
+
 #!/bin/bash
 
-mkdir segmentation
-cp -r ../../segmentation/imagej-threshold-apply-tool ./segmentation/.
+# Change the name of the tool here
+tool_dir="transforms"
+tool_name="imagej-filter-derivativegauss-tool"
 
+# The version is read from the VERSION file
 version=$(<VERSION)
-docker build . -t polusai/imagej-filter-derivativegauss-tool:${version}
+tag="polusai/${tool_name}:${version}"
+echo "Building docker image with tag: ${tag}"
+
+# The current directory and the repository root are saved in variables
+cur_dir=$(pwd)
+repo_root=$(git rev-parse --show-toplevel)
 
-rm -rf ./segmentation
+# The Dockerfile and .dockerignore files are copied to the repository root before building the image
+cd ${repo_root}
+cp ./${tool_dir}/${tool_name}/Dockerfile .
+cp .gitingore .dockerignore
+docker build . -t ${tag}
+rm Dockerfile .dockerignore
+cd ${cur_dir}
diff --git a/transforms/imagej-filter-dog-tool/Dockerfile b/transforms/imagej-filter-dog-tool/Dockerfile
index 14c9bac07..6d468f7b9 100644
--- a/transforms/imagej-filter-dog-tool/Dockerfile
+++ b/transforms/imagej-filter-dog-tool/Dockerfile
@@ -9,29 +9,20 @@ ENV POLUS_LOG="INFO"
 # Work directory defined in the base container
 WORKDIR ${EXEC_DIR}
 
-# ImageJ setup
+# Initialize ImageJ
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
-# Install the ImageJ Threshold Apply tool
-COPY segmentation ${EXEC_DIR}/segmentation
-RUN pip3 install ${EXEC_DIR}/segmentation/imagej-threshold-apply-tool --no-cache-dir
+# TODO: Change the tool_dir to the tool directory
+ENV TOOL_DIR="transforms/imagej-filter-dog-tool"
 
-RUN mkdir ${EXEC_DIR}/transforms
-RUN mkdir ${EXEC_DIR}/transforms/imagej-filter-dog-tool
-WORKDIR ${EXEC_DIR}/transforms/imagej-filter-dog-tool
+# Copy the repository into the container
+RUN mkdir image-tools
+COPY . ${EXEC_DIR}/image-tools
 
-# Install the python package
-COPY pyproject.toml .
-COPY VERSION .
-COPY README.md .
-COPY src ./src
-COPY tests ./tests
-
-RUN pip3 install ${EXEC_DIR}/transforms/imagej-filter-dog-tool --no-cache-dir
-
-RUN pip3 install scikit-image scipy pytest pytest-sugar pytest-json-report --no-cache-dir
-RUN python3 -X faulthandler -m pytest --json-report --json-report-summary -v -p no:faulthandler
-RUN cat .report.json
+# Install the tool
+RUN pip3 install "${EXEC_DIR}/image-tools/${TOOL_DIR}" --no-cache-dir
 
+# Set the entrypoint
+# TODO: Change the entrypoint to the tool entrypoint
 ENTRYPOINT ["python3", "-m", "polus.images.transforms.imagej_filter_dog"]
 CMD ["--help"]
diff --git a/transforms/imagej-filter-dog-tool/build-docker.sh b/transforms/imagej-filter-dog-tool/build-docker.sh
index 8c21fa80a..d13a25837 100755
--- a/transforms/imagej-filter-dog-tool/build-docker.sh
+++ b/transforms/imagej-filter-dog-tool/build-docker.sh
@@ -1,9 +1,23 @@
+
 #!/bin/bash
 
-mkdir segmentation
-cp -r ../../segmentation/imagej-threshold-apply-tool ./segmentation/.
+# Change the name of the tool here
+tool_dir="transforms"
+tool_name="imagej-filter-dog-tool"
 
+# The version is read from the VERSION file
 version=$(<VERSION)
-docker build . -t polusai/imagej-filter-dog-tool:${version}
+tag="polusai/${tool_name}:${version}"
+echo "Building docker image with tag: ${tag}"
+
+# The current directory and the repository root are saved in variables
+cur_dir=$(pwd)
+repo_root=$(git rev-parse --show-toplevel)
 
-rm -rf ./segmentation
+# The Dockerfile and .dockerignore files are copied to the repository root before building the image
+cd ${repo_root}
+cp ./${tool_dir}/${tool_name}/Dockerfile .
+cp .gitingore .dockerignore
+docker build . -t ${tag}
+rm Dockerfile .dockerignore
+cd ${cur_dir}
diff --git a/transforms/imagej-filter-frangivesselness-tool/Dockerfile b/transforms/imagej-filter-frangivesselness-tool/Dockerfile
index 1ab7dfc97..b0a2a4c95 100644
--- a/transforms/imagej-filter-frangivesselness-tool/Dockerfile
+++ b/transforms/imagej-filter-frangivesselness-tool/Dockerfile
@@ -9,29 +9,20 @@ ENV POLUS_LOG="INFO"
 # Work directory defined in the base container
 WORKDIR ${EXEC_DIR}
 
-# ImageJ setup
+# Initialize ImageJ
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
-# Install the ImageJ Threshold Apply tool
-COPY segmentation ${EXEC_DIR}/segmentation
-RUN pip3 install ${EXEC_DIR}/segmentation/imagej-threshold-apply-tool --no-cache-dir
+# TODO: Change the tool_dir to the tool directory
+ENV TOOL_DIR="transforms/imagej-filter-frangivesselness-tool"
 
-RUN mkdir ${EXEC_DIR}/transforms
-RUN mkdir ${EXEC_DIR}/transforms/imagej-filter-frangivesselness-tool
-WORKDIR ${EXEC_DIR}/transforms/imagej-filter-frangivesselness-tool
+# Copy the repository into the container
+RUN mkdir image-tools
+COPY . ${EXEC_DIR}/image-tools
 
-# Install the python package
-COPY pyproject.toml .
-COPY VERSION .
-COPY README.md .
-COPY src ./src
-COPY tests ./tests
-
-RUN pip3 install ${EXEC_DIR}/transforms/imagej-filter-frangivesselness-tool --no-cache-dir
-
-RUN pip3 install scikit-image scipy pytest pytest-sugar pytest-json-report --no-cache-dir
-RUN python3 -X faulthandler -m pytest --json-report --json-report-summary -v -p no:faulthandler
-RUN cat .report.json
+# Install the tool
+RUN pip3 install "${EXEC_DIR}/image-tools/${TOOL_DIR}" --no-cache-dir
 
+# Set the entrypoint
+# TODO: Change the entrypoint to the tool entrypoint
 ENTRYPOINT ["python3", "-m", "polus.images.transforms.imagej_filter_frangivesselness"]
 CMD ["--help"]
diff --git a/transforms/imagej-filter-frangivesselness-tool/build-docker.sh b/transforms/imagej-filter-frangivesselness-tool/build-docker.sh
index a0a3e3f69..4769bba3d 100755
--- a/transforms/imagej-filter-frangivesselness-tool/build-docker.sh
+++ b/transforms/imagej-filter-frangivesselness-tool/build-docker.sh
@@ -1,9 +1,23 @@
+
 #!/bin/bash
 
-mkdir segmentation
-cp -r ../../segmentation/imagej-threshold-apply-tool ./segmentation/.
+# Change the name of the tool here
+tool_dir="transforms"
+tool_name="imagej-filter-frangivesselness-tool"
 
+# The version is read from the VERSION file
 version=$(<VERSION)
-docker build . -t polusai/imagej-filter-frangivesselness-tool:${version}
+tag="polusai/${tool_name}:${version}"
+echo "Building docker image with tag: ${tag}"
+
+# The current directory and the repository root are saved in variables
+cur_dir=$(pwd)
+repo_root=$(git rev-parse --show-toplevel)
 
-rm -rf ./segmentation
+# The Dockerfile and .dockerignore files are copied to the repository root before building the image
+cd ${repo_root}
+cp ./${tool_dir}/${tool_name}/Dockerfile .
+cp .gitingore .dockerignore
+docker build . -t ${tag}
+rm Dockerfile .dockerignore
+cd ${cur_dir}
diff --git a/transforms/imagej-filter-gauss-tool/Dockerfile b/transforms/imagej-filter-gauss-tool/Dockerfile
index 4a5dfb12a..b73bb24e2 100644
--- a/transforms/imagej-filter-gauss-tool/Dockerfile
+++ b/transforms/imagej-filter-gauss-tool/Dockerfile
@@ -9,29 +9,20 @@ ENV POLUS_LOG="INFO"
 # Work directory defined in the base container
 WORKDIR ${EXEC_DIR}
 
-# ImageJ setup
+# Initialize ImageJ
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
-# Install the ImageJ Threshold Apply tool
-COPY segmentation ${EXEC_DIR}/segmentation
-RUN pip3 install ${EXEC_DIR}/segmentation/imagej-threshold-apply-tool --no-cache-dir
+# TODO: Change the tool_dir to the tool directory
+ENV TOOL_DIR="transforms/imagej-filter-gauss-tool"
 
-RUN mkdir ${EXEC_DIR}/transforms
-RUN mkdir ${EXEC_DIR}/transforms/imagej-filter-gauss-tool
-WORKDIR ${EXEC_DIR}/transforms/imagej-filter-gauss-tool
+# Copy the repository into the container
+RUN mkdir image-tools
+COPY . ${EXEC_DIR}/image-tools
 
-# Install the python package
-COPY pyproject.toml .
-COPY VERSION .
-COPY README.md .
-COPY src ./src
-COPY tests ./tests
-
-RUN pip3 install ${EXEC_DIR}/transforms/imagej-filter-gauss-tool --no-cache-dir
-
-RUN pip3 install scikit-image scipy pytest pytest-sugar pytest-json-report --no-cache-dir
-RUN python3 -X faulthandler -m pytest --json-report --json-report-summary -v -p no:faulthandler
-RUN cat .report.json
+# Install the tool
+RUN pip3 install "${EXEC_DIR}/image-tools/${TOOL_DIR}" --no-cache-dir
 
+# Set the entrypoint
+# TODO: Change the entrypoint to the tool entrypoint
 ENTRYPOINT ["python3", "-m", "polus.images.transforms.imagej_filter_gauss"]
 CMD ["--help"]
diff --git a/transforms/imagej-filter-gauss-tool/build-docker.sh b/transforms/imagej-filter-gauss-tool/build-docker.sh
index 391f1863e..9bc9eeb97 100755
--- a/transforms/imagej-filter-gauss-tool/build-docker.sh
+++ b/transforms/imagej-filter-gauss-tool/build-docker.sh
@@ -1,9 +1,23 @@
+
 #!/bin/bash
 
-mkdir segmentation
-cp -r ../../segmentation/imagej-threshold-apply-tool ./segmentation/.
+# Change the name of the tool here
+tool_dir="transforms"
+tool_name="imagej-filter-gauss-tool"
 
+# The version is read from the VERSION file
 version=$(<VERSION)
-docker build . -t polusai/imagej-filter-gauss-tool:${version}
+tag="polusai/${tool_name}:${version}"
+echo "Building docker image with tag: ${tag}"
+
+# The current directory and the repository root are saved in variables
+cur_dir=$(pwd)
+repo_root=$(git rev-parse --show-toplevel)
 
-rm -rf ./segmentation
+# The Dockerfile and .dockerignore files are copied to the repository root before building the image
+cd ${repo_root}
+cp ./${tool_dir}/${tool_name}/Dockerfile .
+cp .gitingore .dockerignore
+docker build . -t ${tag}
+rm Dockerfile .dockerignore
+cd ${cur_dir}
diff --git a/transforms/imagej-filter-partialderivative-tool/Dockerfile b/transforms/imagej-filter-partialderivative-tool/Dockerfile
index 5d9c88d36..53c10e0f8 100644
--- a/transforms/imagej-filter-partialderivative-tool/Dockerfile
+++ b/transforms/imagej-filter-partialderivative-tool/Dockerfile
@@ -9,29 +9,20 @@ ENV POLUS_LOG="INFO"
 # Work directory defined in the base container
 WORKDIR ${EXEC_DIR}
 
-# ImageJ setup
+# Initialize ImageJ
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
-# Install the ImageJ Threshold Apply tool
-COPY segmentation ${EXEC_DIR}/segmentation
-RUN pip3 install ${EXEC_DIR}/segmentation/imagej-threshold-apply-tool --no-cache-dir
+# TODO: Change the tool_dir to the tool directory
+ENV TOOL_DIR="transforms/imagej-filter-partialderivative-tool"
 
-RUN mkdir ${EXEC_DIR}/transforms
-RUN mkdir ${EXEC_DIR}/transforms/imagej-filter-partialderivative-tool
-WORKDIR ${EXEC_DIR}/transforms/imagej-filter-partialderivative-tool
+# Copy the repository into the container
+RUN mkdir image-tools
+COPY . ${EXEC_DIR}/image-tools
 
-# Install the python package
-COPY pyproject.toml .
-COPY VERSION .
-COPY README.md .
-COPY src ./src
-COPY tests ./tests
-
-RUN pip3 install ${EXEC_DIR}/transforms/imagej-filter-partialderivative-tool --no-cache-dir
-
-RUN pip3 install scikit-image scipy pytest pytest-sugar pytest-json-report --no-cache-dir
-RUN python3 -X faulthandler -m pytest --json-report --json-report-summary -v -p no:faulthandler
-RUN cat .report.json
+# Install the tool
+RUN pip3 install "${EXEC_DIR}/image-tools/${TOOL_DIR}" --no-cache-dir
 
+# Set the entrypoint
+# TODO: Change the entrypoint to the tool entrypoint
 ENTRYPOINT ["python3", "-m", "polus.images.transforms.imagej_filter_partialderivative"]
 CMD ["--help"]
diff --git a/transforms/imagej-filter-partialderivative-tool/build-docker.sh b/transforms/imagej-filter-partialderivative-tool/build-docker.sh
index ae92bdf89..91ea94251 100755
--- a/transforms/imagej-filter-partialderivative-tool/build-docker.sh
+++ b/transforms/imagej-filter-partialderivative-tool/build-docker.sh
@@ -1,9 +1,23 @@
+
 #!/bin/bash
 
-mkdir segmentation
-cp -r ../../segmentation/imagej-threshold-apply-tool ./segmentation/.
+# Change the name of the tool here
+tool_dir="transforms"
+tool_name="imagej-filter-partialderivative-tool"
 
+# The version is read from the VERSION file
 version=$(<VERSION)
-docker build . -t polusai/imagej-filter-partialderivative-tool:${version}
+tag="polusai/${tool_name}:${version}"
+echo "Building docker image with tag: ${tag}"
+
+# The current directory and the repository root are saved in variables
+cur_dir=$(pwd)
+repo_root=$(git rev-parse --show-toplevel)
 
-rm -rf ./segmentation
+# The Dockerfile and .dockerignore files are copied to the repository root before building the image
+cd ${repo_root}
+cp ./${tool_dir}/${tool_name}/Dockerfile .
+cp .gitingore .dockerignore
+docker build . -t ${tag}
+rm Dockerfile .dockerignore
+cd ${cur_dir}
diff --git a/transforms/imagej-filter-sobel-tool/Dockerfile b/transforms/imagej-filter-sobel-tool/Dockerfile
index c5c7ae6da..a63185fd8 100644
--- a/transforms/imagej-filter-sobel-tool/Dockerfile
+++ b/transforms/imagej-filter-sobel-tool/Dockerfile
@@ -9,29 +9,20 @@ ENV POLUS_LOG="INFO"
 # Work directory defined in the base container
 WORKDIR ${EXEC_DIR}
 
-# ImageJ setup
+# Initialize ImageJ
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
-# Install the ImageJ Threshold Apply tool
-COPY segmentation ${EXEC_DIR}/segmentation
-RUN pip3 install ${EXEC_DIR}/segmentation/imagej-threshold-apply-tool --no-cache-dir
+# TODO: Change the tool_dir to the tool directory
+ENV TOOL_DIR="transforms/imagej-filter-sobel-tool"
 
-RUN mkdir ${EXEC_DIR}/transforms
-RUN mkdir ${EXEC_DIR}/transforms/imagej-filter-sobel-tool
-WORKDIR ${EXEC_DIR}/transforms/imagej-filter-sobel-tool
+# Copy the repository into the container
+RUN mkdir image-tools
+COPY . ${EXEC_DIR}/image-tools
 
-# Install the python package
-COPY pyproject.toml .
-COPY VERSION .
-COPY README.md .
-COPY src ./src
-COPY tests ./tests
-
-RUN pip3 install ${EXEC_DIR}/transforms/imagej-filter-sobel-tool --no-cache-dir
-
-RUN pip3 install scikit-image scipy pytest pytest-sugar pytest-json-report --no-cache-dir
-RUN python3 -X faulthandler -m pytest --json-report --json-report-summary -v -p no:faulthandler
-RUN cat .report.json
+# Install the tool
+RUN pip3 install "${EXEC_DIR}/image-tools/${TOOL_DIR}" --no-cache-dir
 
+# Set the entrypoint
+# TODO: Change the entrypoint to the tool entrypoint
 ENTRYPOINT ["python3", "-m", "polus.images.transforms.imagej_filter_sobel"]
 CMD ["--help"]
diff --git a/transforms/imagej-filter-sobel-tool/build-docker.sh b/transforms/imagej-filter-sobel-tool/build-docker.sh
index b5f15aaa2..b7d829468 100755
--- a/transforms/imagej-filter-sobel-tool/build-docker.sh
+++ b/transforms/imagej-filter-sobel-tool/build-docker.sh
@@ -1,9 +1,23 @@
+
 #!/bin/bash
 
-mkdir segmentation
-cp -r ../../segmentation/imagej-threshold-apply-tool ./segmentation/.
+# Change the name of the tool here
+tool_dir="transforms"
+tool_name="imagej-filter-sobel-tool"
 
+# The version is read from the VERSION file
 version=$(<VERSION)
-docker build . -t polusai/imagej-filter-sobel-tool:${version}
+tag="polusai/${tool_name}:${version}"
+echo "Building docker image with tag: ${tag}"
+
+# The current directory and the repository root are saved in variables
+cur_dir=$(pwd)
+repo_root=$(git rev-parse --show-toplevel)
 
-rm -rf ./segmentation
+# The Dockerfile and .dockerignore files are copied to the repository root before building the image
+cd ${repo_root}
+cp ./${tool_dir}/${tool_name}/Dockerfile .
+cp .gitingore .dockerignore
+docker build . -t ${tag}
+rm Dockerfile .dockerignore
+cd ${cur_dir}
diff --git a/transforms/imagej-filter-tubeness-tool/Dockerfile b/transforms/imagej-filter-tubeness-tool/Dockerfile
index 69bcca5fc..9db75d90a 100644
--- a/transforms/imagej-filter-tubeness-tool/Dockerfile
+++ b/transforms/imagej-filter-tubeness-tool/Dockerfile
@@ -9,29 +9,20 @@ ENV POLUS_LOG="INFO"
 # Work directory defined in the base container
 WORKDIR ${EXEC_DIR}
 
-# ImageJ setup
+# Initialize ImageJ
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
-# Install the ImageJ Threshold Apply tool
-COPY segmentation ${EXEC_DIR}/segmentation
-RUN pip3 install ${EXEC_DIR}/segmentation/imagej-threshold-apply-tool --no-cache-dir
+# TODO: Change the tool_dir to the tool directory
+ENV TOOL_DIR="transforms/imagej-filter-tubeness-tool"
 
-RUN mkdir ${EXEC_DIR}/transforms
-RUN mkdir ${EXEC_DIR}/transforms/imagej-filter-tubeness-tool
-WORKDIR ${EXEC_DIR}/transforms/imagej-filter-tubeness-tool
+# Copy the repository into the container
+RUN mkdir image-tools
+COPY . ${EXEC_DIR}/image-tools
 
-# Install the python package
-COPY pyproject.toml .
-COPY VERSION .
-COPY README.md .
-COPY src ./src
-COPY tests ./tests
-
-RUN pip3 install ${EXEC_DIR}/transforms/imagej-filter-tubeness-tool --no-cache-dir
-
-RUN pip3 install scikit-image scipy pytest pytest-sugar pytest-json-report --no-cache-dir
-RUN python3 -X faulthandler -m pytest --json-report --json-report-summary -v -p no:faulthandler
-RUN cat .report.json
+# Install the tool
+RUN pip3 install "${EXEC_DIR}/image-tools/${TOOL_DIR}" --no-cache-dir
 
+# Set the entrypoint
+# TODO: Change the entrypoint to the tool entrypoint
 ENTRYPOINT ["python3", "-m", "polus.images.transforms.imagej_filter_tubeness"]
 CMD ["--help"]
diff --git a/transforms/imagej-filter-tubeness-tool/build-docker.sh b/transforms/imagej-filter-tubeness-tool/build-docker.sh
index 4a5162de0..414fe93b9 100755
--- a/transforms/imagej-filter-tubeness-tool/build-docker.sh
+++ b/transforms/imagej-filter-tubeness-tool/build-docker.sh
@@ -1,9 +1,23 @@
+
 #!/bin/bash
 
-mkdir segmentation
-cp -r ../../segmentation/imagej-threshold-apply-tool ./segmentation/.
+# Change the name of the tool here
+tool_dir="transforms"
+tool_name="imagej-filter-tubeness-tool"
 
+# The version is read from the VERSION file
 version=$(<VERSION)
-docker build . -t polusai/imagej-filter-tubeness-tool:${version}
+tag="polusai/${tool_name}:${version}"
+echo "Building docker image with tag: ${tag}"
+
+# The current directory and the repository root are saved in variables
+cur_dir=$(pwd)
+repo_root=$(git rev-parse --show-toplevel)
 
-rm -rf ./segmentation
+# The Dockerfile and .dockerignore files are copied to the repository root before building the image
+cd ${repo_root}
+cp ./${tool_dir}/${tool_name}/Dockerfile .
+cp .gitingore .dockerignore
+docker build . -t ${tag}
+rm Dockerfile .dockerignore
+cd ${cur_dir}
diff --git a/transforms/imagej-image-integral-tool/Dockerfile b/transforms/imagej-image-integral-tool/Dockerfile
index 055518a68..6a70ccedc 100644
--- a/transforms/imagej-image-integral-tool/Dockerfile
+++ b/transforms/imagej-image-integral-tool/Dockerfile
@@ -9,29 +9,20 @@ ENV POLUS_LOG="INFO"
 # Work directory defined in the base container
 WORKDIR ${EXEC_DIR}
 
-# ImageJ setup
+# Initialize ImageJ
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
-# Install the ImageJ Threshold Apply tool
-COPY segmentation ${EXEC_DIR}/segmentation
-RUN pip3 install ${EXEC_DIR}/segmentation/imagej-threshold-apply-tool --no-cache-dir
+# TODO: Change the tool_dir to the tool directory
+ENV TOOL_DIR="transforms/imagej-image-integral-tool"
 
-RUN mkdir ${EXEC_DIR}/transforms
-RUN mkdir ${EXEC_DIR}/transforms/imagej-image-integral-tool
-WORKDIR ${EXEC_DIR}/transforms/imagej-image-integral-tool
+# Copy the repository into the container
+RUN mkdir image-tools
+COPY . ${EXEC_DIR}/image-tools
 
-# Install the python package
-COPY pyproject.toml .
-COPY VERSION .
-COPY README.md .
-COPY src ./src
-COPY tests ./tests
-
-RUN pip3 install ${EXEC_DIR}/transforms/imagej-image-integral-tool --no-cache-dir
-
-RUN pip3 install scikit-image scipy pytest pytest-sugar pytest-json-report --no-cache-dir
-RUN python3 -X faulthandler -m pytest --json-report --json-report-summary -v -p no:faulthandler
-RUN cat .report.json
+# Install the tool
+RUN pip3 install "${EXEC_DIR}/image-tools/${TOOL_DIR}" --no-cache-dir
 
+# Set the entrypoint
+# TODO: Change the entrypoint to the tool entrypoint
 ENTRYPOINT ["python3", "-m", "polus.images.transforms.imagej_image_integral"]
 CMD ["--help"]
diff --git a/transforms/imagej-image-integral-tool/build-docker.sh b/transforms/imagej-image-integral-tool/build-docker.sh
index aebad03a5..5cdc35873 100755
--- a/transforms/imagej-image-integral-tool/build-docker.sh
+++ b/transforms/imagej-image-integral-tool/build-docker.sh
@@ -1,9 +1,23 @@
+
 #!/bin/bash
 
-mkdir segmentation
-cp -r ../../segmentation/imagej-threshold-apply-tool ./segmentation/.
+# Change the name of the tool here
+tool_dir="transforms"
+tool_name="imagej-image-integral-tool"
 
+# The version is read from the VERSION file
 version=$(<VERSION)
-docker build . -t polusai/imagej-image-integral-tool:${version}
+tag="polusai/${tool_name}:${version}"
+echo "Building docker image with tag: ${tag}"
+
+# The current directory and the repository root are saved in variables
+cur_dir=$(pwd)
+repo_root=$(git rev-parse --show-toplevel)
 
-rm -rf ./segmentation
+# The Dockerfile and .dockerignore files are copied to the repository root before building the image
+cd ${repo_root}
+cp ./${tool_dir}/${tool_name}/Dockerfile .
+cp .gitingore .dockerignore
+docker build . -t ${tag}
+rm Dockerfile .dockerignore
+cd ${cur_dir}
diff --git a/transforms/imagej-image-invert-tool/Dockerfile b/transforms/imagej-image-invert-tool/Dockerfile
index 5af672dc6..2c498bf0d 100644
--- a/transforms/imagej-image-invert-tool/Dockerfile
+++ b/transforms/imagej-image-invert-tool/Dockerfile
@@ -9,29 +9,20 @@ ENV POLUS_LOG="INFO"
 # Work directory defined in the base container
 WORKDIR ${EXEC_DIR}
 
-# ImageJ setup
+# Initialize ImageJ
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
-# Install the ImageJ Threshold Apply tool
-COPY segmentation ${EXEC_DIR}/segmentation
-RUN pip3 install ${EXEC_DIR}/segmentation/imagej-threshold-apply-tool --no-cache-dir
+# TODO: Change the tool_dir to the tool directory
+ENV TOOL_DIR="transforms/imagej-image-invert-tool"
 
-RUN mkdir ${EXEC_DIR}/transforms
-RUN mkdir ${EXEC_DIR}/transforms/imagej-image-invert-tool
-WORKDIR ${EXEC_DIR}/transforms/imagej-image-invert-tool
+# Copy the repository into the container
+RUN mkdir image-tools
+COPY . ${EXEC_DIR}/image-tools
 
-# Install the python package
-COPY pyproject.toml .
-COPY VERSION .
-COPY README.md .
-COPY src ./src
-COPY tests ./tests
-
-RUN pip3 install ${EXEC_DIR}/transforms/imagej-image-invert-tool --no-cache-dir
-
-RUN pip3 install scikit-image scipy pytest pytest-sugar pytest-json-report --no-cache-dir
-RUN python3 -X faulthandler -m pytest --json-report --json-report-summary -v -p no:faulthandler
-RUN cat .report.json
+# Install the tool
+RUN pip3 install "${EXEC_DIR}/image-tools/${TOOL_DIR}" --no-cache-dir
 
+# Set the entrypoint
+# TODO: Change the entrypoint to the tool entrypoint
 ENTRYPOINT ["python3", "-m", "polus.images.transforms.imagej_image_invert"]
 CMD ["--help"]
diff --git a/transforms/imagej-image-invert-tool/build-docker.sh b/transforms/imagej-image-invert-tool/build-docker.sh
index 5cf487956..2fdf788af 100755
--- a/transforms/imagej-image-invert-tool/build-docker.sh
+++ b/transforms/imagej-image-invert-tool/build-docker.sh
@@ -1,9 +1,23 @@
+
 #!/bin/bash
 
-mkdir segmentation
-cp -r ../../segmentation/imagej-threshold-apply-tool ./segmentation/.
+# Change the name of the tool here
+tool_dir="transforms"
+tool_name="imagej-image-invert-tool"
 
+# The version is read from the VERSION file
 version=$(<VERSION)
-docker build . -t polusai/imagej-image-invert-tool:${version}
+tag="polusai/${tool_name}:${version}"
+echo "Building docker image with tag: ${tag}"
+
+# The current directory and the repository root are saved in variables
+cur_dir=$(pwd)
+repo_root=$(git rev-parse --show-toplevel)
 
-rm -rf ./segmentation
+# The Dockerfile and .dockerignore files are copied to the repository root before building the image
+cd ${repo_root}
+cp ./${tool_dir}/${tool_name}/Dockerfile .
+cp .gitingore .dockerignore
+docker build . -t ${tag}
+rm Dockerfile .dockerignore
+cd ${cur_dir}
diff --git a/transforms/images/apply-flatfield-tool/Dockerfile b/transforms/images/apply-flatfield-tool/Dockerfile
index 4e3be68d8..b05d29200 100644
--- a/transforms/images/apply-flatfield-tool/Dockerfile
+++ b/transforms/images/apply-flatfield-tool/Dockerfile
@@ -9,12 +9,17 @@ ENV POLUS_LOG="INFO"
 # Work directory defined in the base container
 WORKDIR ${EXEC_DIR}
 
-COPY pyproject.toml ${EXEC_DIR}
-COPY VERSION ${EXEC_DIR}
-COPY README.md ${EXEC_DIR}
-COPY src ${EXEC_DIR}/src
+# TODO: Change the tool_dir to the tool directory
+ENV TOOL_DIR="transforms/images/apply-flatfield-tool"
 
-RUN pip3 install ${EXEC_DIR} --no-cache-dir
+# Copy the repository into the container
+RUN mkdir image-tools
+COPY . ${EXEC_DIR}/image-tools
 
+# Install the tool
+RUN pip3 install "${EXEC_DIR}/image-tools/${TOOL_DIR}" --no-cache-dir
+
+# Set the entrypoint
+# TODO: Change the entrypoint to the tool entrypoint
 ENTRYPOINT ["python3", "-m", "polus.images.transforms.images.apply_flatfield"]
 CMD ["--help"]
diff --git a/transforms/images/apply-flatfield-tool/build-docker.sh b/transforms/images/apply-flatfield-tool/build-docker.sh
index 3d0ade47b..975253b70 100644
--- a/transforms/images/apply-flatfield-tool/build-docker.sh
+++ b/transforms/images/apply-flatfield-tool/build-docker.sh
@@ -1,4 +1,23 @@
+
 #!/bin/bash
 
+# Change the name of the tool here
+tool_dir="transforms/images"
+tool_name="apply-flatfield-tool"
+
+# The version is read from the VERSION file
 version=$(<VERSION)
-docker build . -t polusai/apply-flatfield-tool:${version}
+tag="polusai/${tool_name}:${version}"
+echo "Building docker image with tag: ${tag}"
+
+# The current directory and the repository root are saved in variables
+cur_dir=$(pwd)
+repo_root=$(git rev-parse --show-toplevel)
+
+# The Dockerfile and .dockerignore files are copied to the repository root before building the image
+cd ${repo_root}
+cp ./${tool_dir}/${tool_name}/Dockerfile .
+cp .gitingore .dockerignore
+docker build . -t ${tag}
+rm Dockerfile .dockerignore
+cd ${cur_dir}
diff --git a/transforms/images/binary-operations-tool/Dockerfile b/transforms/images/binary-operations-tool/Dockerfile
index 8db44f987..8aa42a787 100644
--- a/transforms/images/binary-operations-tool/Dockerfile
+++ b/transforms/images/binary-operations-tool/Dockerfile
@@ -1,23 +1,25 @@
 FROM polusai/bfio:2.1.9
 
 # environment variables defined in polusai/bfio
-# ENV EXEC_DIR="/opt/executables"
-# ENV DATA_DIR="/data"
-# ENV POLUS_EXT=".ome.tif"
-# ENV POLUS_LOG="INFO" # Change to WARNING for fewer logs, and DEBUG for debugging
+ENV EXEC_DIR="/opt/executables"
 ENV POLUS_IMG_EXT=".ome.tif"
 ENV POLUS_TAB_EXT=".csv"
+ENV POLUS_LOG="INFO"
 
 # Work directory defined in the base container
-# WORKDIR ${EXEC_DIR}
+WORKDIR ${EXEC_DIR}
 
-COPY pyproject.toml ${EXEC_DIR}
-COPY VERSION ${EXEC_DIR}
-COPY README.md ${EXEC_DIR}
-RUN pip3 install --index-url https://test.pypi.org/simple/ filepattern==2.2.7
-COPY src ${EXEC_DIR}/src
+# TODO: Change the tool_dir to the tool directory
+ENV TOOL_DIR="transforms/images/binary-operations-tool"
 
-RUN pip3 install ${EXEC_DIR} --no-cache-dir
+# Copy the repository into the container
+RUN mkdir image-tools
+COPY . ${EXEC_DIR}/image-tools
 
+# Install the tool
+RUN pip3 install "${EXEC_DIR}/image-tools/${TOOL_DIR}" --no-cache-dir
+
+# Set the entrypoint
+# TODO: Change the entrypoint to the tool entrypoint
 ENTRYPOINT ["python3", "-m", "polus.images.transforms.images.binary_operations"]
 CMD ["--help"]
diff --git a/transforms/images/binary-operations-tool/build-docker.sh b/transforms/images/binary-operations-tool/build-docker.sh
index 73642e7d6..866160a47 100755
--- a/transforms/images/binary-operations-tool/build-docker.sh
+++ b/transforms/images/binary-operations-tool/build-docker.sh
@@ -1,4 +1,23 @@
+
 #!/bin/bash
 
+# Change the name of the tool here
+tool_dir="transforms/images"
+tool_name="binary-operations-tool"
+
+# The version is read from the VERSION file
 version=$(<VERSION)
-docker build . -t polusai/binary-operations-tool:"${version}"
+tag="polusai/${tool_name}:${version}"
+echo "Building docker image with tag: ${tag}"
+
+# The current directory and the repository root are saved in variables
+cur_dir=$(pwd)
+repo_root=$(git rev-parse --show-toplevel)
+
+# The Dockerfile and .dockerignore files are copied to the repository root before building the image
+cd ${repo_root}
+cp ./${tool_dir}/${tool_name}/Dockerfile .
+cp .gitingore .dockerignore
+docker build . -t ${tag}
+rm Dockerfile .dockerignore
+cd ${cur_dir}
diff --git a/transforms/images/image-assembler-tool/Dockerfile b/transforms/images/image-assembler-tool/Dockerfile
index f3dc7bccc..edec6a2b4 100644
--- a/transforms/images/image-assembler-tool/Dockerfile
+++ b/transforms/images/image-assembler-tool/Dockerfile
@@ -1,27 +1,25 @@
 FROM polusai/bfio:2.3.3
 
 # environment variables defined in polusai/bfio
-# ENV EXEC_DIR="/opt/executables"
-# ENV DATA_DIR="/data"
-# ENV POLUS_EXT=".ome.tif"
-
-#Change to WARNING for fewer logs, and DEBUG for debugging
-ENV POLUS_LOG="INFO"
-
+ENV EXEC_DIR="/opt/executables"
 ENV POLUS_IMG_EXT=".ome.tif"
 ENV POLUS_TAB_EXT=".csv"
+ENV POLUS_LOG="INFO"
 
 # Work directory defined in the base container
-# WORKDIR ${EXEC_DIR}
+WORKDIR ${EXEC_DIR}
+
+# TODO: Change the tool_dir to the tool directory
+ENV TOOL_DIR="transforms/images/image-assembler-tool"
 
-COPY pyproject.toml ${EXEC_DIR}
-COPY VERSION ${EXEC_DIR}
-COPY README.md ${EXEC_DIR}
-COPY CHANGELOG.md ${EXEC_DIR}
-COPY src ${EXEC_DIR}/src
+# Copy the repository into the container
+RUN mkdir image-tools
+COPY . ${EXEC_DIR}/image-tools
 
-RUN pip3 install ${EXEC_DIR} --no-cache-dir
+# Install the tool
+RUN pip3 install "${EXEC_DIR}/image-tools/${TOOL_DIR}" --no-cache-dir
 
-# Default command. Additional arguments are provided through the command line
+# Set the entrypoint
+# TODO: Change the entrypoint to the tool entrypoint
 ENTRYPOINT ["python3", "-m", "polus.images.transforms.images.image_assembler"]
 CMD ["--help"]
diff --git a/transforms/images/image-assembler-tool/build-docker.sh b/transforms/images/image-assembler-tool/build-docker.sh
index 1b491d1d9..28a871eb0 100755
--- a/transforms/images/image-assembler-tool/build-docker.sh
+++ b/transforms/images/image-assembler-tool/build-docker.sh
@@ -1,4 +1,23 @@
+
 #!/bin/bash
 
+# Change the name of the tool here
+tool_dir="transforms/images"
+tool_name="image-assembler-tool"
+
+# The version is read from the VERSION file
 version=$(<VERSION)
-docker build . -t polusai/image-assembler-tool:${version}
+tag="polusai/${tool_name}:${version}"
+echo "Building docker image with tag: ${tag}"
+
+# The current directory and the repository root are saved in variables
+cur_dir=$(pwd)
+repo_root=$(git rev-parse --show-toplevel)
+
+# The Dockerfile and .dockerignore files are copied to the repository root before building the image
+cd ${repo_root}
+cp ./${tool_dir}/${tool_name}/Dockerfile .
+cp .gitingore .dockerignore
+docker build . -t ${tag}
+rm Dockerfile .dockerignore
+cd ${cur_dir}
diff --git a/transforms/images/image-calculator-tool/Dockerfile b/transforms/images/image-calculator-tool/Dockerfile
index 4f96ca9cd..89ec07df5 100644
--- a/transforms/images/image-calculator-tool/Dockerfile
+++ b/transforms/images/image-calculator-tool/Dockerfile
@@ -2,22 +2,24 @@ FROM polusai/bfio:2.1.9
 
 # environment variables defined in polusai/bfio
 ENV EXEC_DIR="/opt/executables"
-ENV DATA_DIR="/data"
-ENV POLUS_LOG="INFO"
 ENV POLUS_IMG_EXT=".ome.tif"
 ENV POLUS_TAB_EXT=".csv"
-
-RUN mkdir /.cache && chmod 777 /.cache
+ENV POLUS_LOG="INFO"
 
 # Work directory defined in the base container
 WORKDIR ${EXEC_DIR}
 
-COPY pyproject.toml ${EXEC_DIR}
-COPY VERSION ${EXEC_DIR}
-COPY README.md ${EXEC_DIR}
-COPY src ${EXEC_DIR}/src
+# TODO: Change the tool_dir to the tool directory
+ENV TOOL_DIR="transforms/images/image-calculator-tool"
+
+# Copy the repository into the container
+RUN mkdir image-tools
+COPY . ${EXEC_DIR}/image-tools
 
-RUN pip3 install ${EXEC_DIR} --no-cache-dir
+# Install the tool
+RUN pip3 install "${EXEC_DIR}/image-tools/${TOOL_DIR}" --no-cache-dir
 
+# Set the entrypoint
+# TODO: Change the entrypoint to the tool entrypoint
 ENTRYPOINT ["python3", "-m", "polus.images.transforms.images.image_calculator"]
 CMD ["--help"]
diff --git a/transforms/images/image-calculator-tool/build-docker.sh b/transforms/images/image-calculator-tool/build-docker.sh
index 01d49cdfe..94f3ae9fb 100755
--- a/transforms/images/image-calculator-tool/build-docker.sh
+++ b/transforms/images/image-calculator-tool/build-docker.sh
@@ -1,4 +1,23 @@
+
 #!/bin/bash
 
+# Change the name of the tool here
+tool_dir="transforms/images"
+tool_name="image-calculator-tool"
+
+# The version is read from the VERSION file
 version=$(<VERSION)
-docker build . -t polusai/image-calculator-tool:"${version}"
+tag="polusai/${tool_name}:${version}"
+echo "Building docker image with tag: ${tag}"
+
+# The current directory and the repository root are saved in variables
+cur_dir=$(pwd)
+repo_root=$(git rev-parse --show-toplevel)
+
+# The Dockerfile and .dockerignore files are copied to the repository root before building the image
+cd ${repo_root}
+cp ./${tool_dir}/${tool_name}/Dockerfile .
+cp .gitingore .dockerignore
+docker build . -t ${tag}
+rm Dockerfile .dockerignore
+cd ${cur_dir}
diff --git a/transforms/images/lumos-bleedthrough-correction-tool/Dockerfile b/transforms/images/lumos-bleedthrough-correction-tool/Dockerfile
index 30a5adad9..86e46df87 100644
--- a/transforms/images/lumos-bleedthrough-correction-tool/Dockerfile
+++ b/transforms/images/lumos-bleedthrough-correction-tool/Dockerfile
@@ -2,22 +2,24 @@ FROM polusai/bfio:2.1.9
 
 # environment variables defined in polusai/bfio
 ENV EXEC_DIR="/opt/executables"
-ENV DATA_DIR="/data"
-ENV POLUS_EXT=".ome.tif"
-# Change to WARNING for fewer logs, and DEBUG for debugging
-ENV POLUS_LOG="INFO"
 ENV POLUS_IMG_EXT=".ome.tif"
 ENV POLUS_TAB_EXT=".csv"
+ENV POLUS_LOG="INFO"
 
 # Work directory defined in the base container
 WORKDIR ${EXEC_DIR}
 
-COPY pyproject.toml ${EXEC_DIR}
-COPY VERSION ${EXEC_DIR}
-COPY README.md ${EXEC_DIR}
-COPY src ${EXEC_DIR}/src
+# TODO: Change the tool_dir to the tool directory
+ENV TOOL_DIR="transforms/images/lumos-bleedthrough-correction-tool"
+
+# Copy the repository into the container
+RUN mkdir image-tools
+COPY . ${EXEC_DIR}/image-tools
 
-RUN pip3 install ${EXEC_DIR} --no-cache-dir
+# Install the tool
+RUN pip3 install "${EXEC_DIR}/image-tools/${TOOL_DIR}" --no-cache-dir
 
+# Set the entrypoint
+# TODO: Change the entrypoint to the tool entrypoint
 ENTRYPOINT ["python3", "-m", "polus.images.transforms.images.lumos_bleedthrough_correction"]
 CMD ["--help"]
diff --git a/transforms/images/lumos-bleedthrough-correction-tool/build-docker.sh b/transforms/images/lumos-bleedthrough-correction-tool/build-docker.sh
index 3deeda1de..9233954b2 100755
--- a/transforms/images/lumos-bleedthrough-correction-tool/build-docker.sh
+++ b/transforms/images/lumos-bleedthrough-correction-tool/build-docker.sh
@@ -1,4 +1,23 @@
+
 #!/bin/bash
 
+# Change the name of the tool here
+tool_dir="transforms/images"
+tool_name="lumos-bleedthrough-correction-tool"
+
+# The version is read from the VERSION file
 version=$(<VERSION)
-docker build . -t polusai/lumos-bleedthrough-correction-tool:"${version}"
+tag="polusai/${tool_name}:${version}"
+echo "Building docker image with tag: ${tag}"
+
+# The current directory and the repository root are saved in variables
+cur_dir=$(pwd)
+repo_root=$(git rev-parse --show-toplevel)
+
+# The Dockerfile and .dockerignore files are copied to the repository root before building the image
+cd ${repo_root}
+cp ./${tool_dir}/${tool_name}/Dockerfile .
+cp .gitingore .dockerignore
+docker build . -t ${tag}
+rm Dockerfile .dockerignore
+cd ${cur_dir}
diff --git a/transforms/images/montage-tool/Dockerfile b/transforms/images/montage-tool/Dockerfile
index 73179903f..35b58c4c7 100644
--- a/transforms/images/montage-tool/Dockerfile
+++ b/transforms/images/montage-tool/Dockerfile
@@ -1,22 +1,25 @@
 FROM polusai/bfio:2.1.9
 
 # environment variables defined in polusai/bfio
-# ENV EXEC_DIR="/opt/executables"
-# ENV DATA_DIR="/data"
-# ENV POLUS_EXT=".ome.tif"
-# ENV POLUS_LOG="INFO" # Change to WARNING for fewer logs, and DEBUG for debugging
+ENV EXEC_DIR="/opt/executables"
 ENV POLUS_IMG_EXT=".ome.tif"
 ENV POLUS_TAB_EXT=".csv"
+ENV POLUS_LOG="INFO"
 
 # Work directory defined in the base container
-# WORKDIR ${EXEC_DIR}
+WORKDIR ${EXEC_DIR}
 
-COPY pyproject.toml ${EXEC_DIR}
-COPY VERSION ${EXEC_DIR}
-COPY README.md ${EXEC_DIR}
-COPY src ${EXEC_DIR}/src
+# TODO: Change the tool_dir to the tool directory
+ENV TOOL_DIR="transforms/images/montage-tool"
 
-RUN pip3 install ${EXEC_DIR} --no-cache-dir
+# Copy the repository into the container
+RUN mkdir image-tools
+COPY . ${EXEC_DIR}/image-tools
 
+# Install the tool
+RUN pip3 install "${EXEC_DIR}/image-tools/${TOOL_DIR}" --no-cache-dir
+
+# Set the entrypoint
+# TODO: Change the entrypoint to the tool entrypoint
 ENTRYPOINT ["python3", "-m", "polus.images.transforms.images.montage"]
 CMD ["--help"]
diff --git a/transforms/images/montage-tool/build-docker.sh b/transforms/images/montage-tool/build-docker.sh
index 4ba1d08b4..134ae4140 100755
--- a/transforms/images/montage-tool/build-docker.sh
+++ b/transforms/images/montage-tool/build-docker.sh
@@ -1,4 +1,23 @@
+
 #!/bin/bash
 
+# Change the name of the tool here
+tool_dir="transforms/images"
+tool_name="montage-tool"
+
+# The version is read from the VERSION file
 version=$(<VERSION)
-docker build . -t polusai/montage-tool:"${version}"
+tag="polusai/${tool_name}:${version}"
+echo "Building docker image with tag: ${tag}"
+
+# The current directory and the repository root are saved in variables
+cur_dir=$(pwd)
+repo_root=$(git rev-parse --show-toplevel)
+
+# The Dockerfile and .dockerignore files are copied to the repository root before building the image
+cd ${repo_root}
+cp ./${tool_dir}/${tool_name}/Dockerfile .
+cp .gitingore .dockerignore
+docker build . -t ${tag}
+rm Dockerfile .dockerignore
+cd ${cur_dir}
diff --git a/transforms/images/roi-relabel-tool/Dockerfile b/transforms/images/roi-relabel-tool/Dockerfile
index 79fbeb8be..f45d66639 100644
--- a/transforms/images/roi-relabel-tool/Dockerfile
+++ b/transforms/images/roi-relabel-tool/Dockerfile
@@ -1,22 +1,25 @@
 FROM polusai/bfio:2.1.9
 
 # environment variables defined in polusai/bfio
-# ENV EXEC_DIR="/opt/executables"
-# ENV DATA_DIR="/data"
-# ENV POLUS_EXT=".ome.tif"
-# ENV POLUS_LOG="INFO" # Change to WARNING for fewer logs, and DEBUG for debugging
+ENV EXEC_DIR="/opt/executables"
 ENV POLUS_IMG_EXT=".ome.tif"
 ENV POLUS_TAB_EXT=".csv"
+ENV POLUS_LOG="INFO"
 
 # Work directory defined in the base container
-# WORKDIR ${EXEC_DIR}
+WORKDIR ${EXEC_DIR}
 
-COPY pyproject.toml ${EXEC_DIR}
-COPY VERSION ${EXEC_DIR}
-COPY README.md ${EXEC_DIR}
-COPY src ${EXEC_DIR}/src
+# TODO: Change the tool_dir to the tool directory
+ENV TOOL_DIR="transforms/images/roi-relabel-tool"
 
-RUN pip3 install ${EXEC_DIR} --no-cache-dir
+# Copy the repository into the container
+RUN mkdir image-tools
+COPY . ${EXEC_DIR}/image-tools
 
+# Install the tool
+RUN pip3 install "${EXEC_DIR}/image-tools/${TOOL_DIR}" --no-cache-dir
+
+# Set the entrypoint
+# TODO: Change the entrypoint to the tool entrypoint
 ENTRYPOINT ["python3", "-m", "polus.images.transforms.images.roi_relabel"]
 CMD ["--help"]
diff --git a/transforms/images/roi-relabel-tool/build-docker.sh b/transforms/images/roi-relabel-tool/build-docker.sh
index ab3559ce1..134354f40 100755
--- a/transforms/images/roi-relabel-tool/build-docker.sh
+++ b/transforms/images/roi-relabel-tool/build-docker.sh
@@ -1,5 +1,23 @@
+
 #!/bin/bash
 
+# Change the name of the tool here
+tool_dir="transforms/images"
+tool_name="roi-relabel-tool"
+
+# The version is read from the VERSION file
 version=$(<VERSION)
+tag="polusai/${tool_name}:${version}"
+echo "Building docker image with tag: ${tag}"
+
+# The current directory and the repository root are saved in variables
+cur_dir=$(pwd)
+repo_root=$(git rev-parse --show-toplevel)
 
-docker build . -t polusai/roi-relabel-tool:"${version}"
+# The Dockerfile and .dockerignore files are copied to the repository root before building the image
+cd ${repo_root}
+cp ./${tool_dir}/${tool_name}/Dockerfile .
+cp .gitingore .dockerignore
+docker build . -t ${tag}
+rm Dockerfile .dockerignore
+cd ${cur_dir}
diff --git a/utils/rxiv-download-tool/Dockerfile b/utils/rxiv-download-tool/Dockerfile
index 13e824227..c9d78f6b7 100644
--- a/utils/rxiv-download-tool/Dockerfile
+++ b/utils/rxiv-download-tool/Dockerfile
@@ -4,17 +4,22 @@ FROM polusai/bfio:2.3.6
 ENV EXEC_DIR="/opt/executables"
 ENV POLUS_IMG_EXT=".ome.tif"
 ENV POLUS_TAB_EXT=".csv"
-ENV POLUS_EXT=".xml"
+ENV POLUS_LOG="INFO"
 
 # Work directory defined in the base container
 WORKDIR ${EXEC_DIR}
 
-COPY pyproject.toml ${EXEC_DIR}
-COPY VERSION ${EXEC_DIR}
-COPY README.md ${EXEC_DIR}
-COPY src ${EXEC_DIR}/src
+# TODO: Change the tool_dir to the tool directory
+ENV TOOL_DIR="utils/rxiv-download-tool"
 
-RUN pip3 install ${EXEC_DIR} --no-cache-dir
+# Copy the repository into the container
+RUN mkdir image-tools
+COPY . ${EXEC_DIR}/image-tools
 
+# Install the tool
+RUN pip3 install "${EXEC_DIR}/image-tools/${TOOL_DIR}" --no-cache-dir
+
+# Set the entrypoint
+# TODO: Change the entrypoint to the tool entrypoint
 ENTRYPOINT ["python3", "-m", "polus.images.utils.rxiv_download"]
 CMD ["--help"]
diff --git a/utils/rxiv-download-tool/build-docker.sh b/utils/rxiv-download-tool/build-docker.sh
index a5b03c6e1..18ed27298 100644
--- a/utils/rxiv-download-tool/build-docker.sh
+++ b/utils/rxiv-download-tool/build-docker.sh
@@ -1,4 +1,23 @@
+
 #!/bin/bash
 
+# Change the name of the tool here
+tool_dir="utils"
+tool_name="rxiv-download-tool"
+
+# The version is read from the VERSION file
 version=$(<VERSION)
-docker build . -t polusai/rxiv-download-tool:${version}
+tag="polusai/${tool_name}:${version}"
+echo "Building docker image with tag: ${tag}"
+
+# The current directory and the repository root are saved in variables
+cur_dir=$(pwd)
+repo_root=$(git rev-parse --show-toplevel)
+
+# The Dockerfile and .dockerignore files are copied to the repository root before building the image
+cd ${repo_root}
+cp ./${tool_dir}/${tool_name}/Dockerfile .
+cp .gitingore .dockerignore
+docker build . -t ${tag}
+rm Dockerfile .dockerignore
+cd ${cur_dir}
diff --git a/visualization/microjson-to-ome-tool/Dockerfile b/visualization/microjson-to-ome-tool/Dockerfile
index c06c538a4..78b59febb 100644
--- a/visualization/microjson-to-ome-tool/Dockerfile
+++ b/visualization/microjson-to-ome-tool/Dockerfile
@@ -1,26 +1,25 @@
 FROM polusai/bfio:2.3.3
 
 # environment variables defined in polusai/bfio
-# ENV EXEC_DIR="/opt/executables"
-# ENV DATA_DIR="/data"
-# ENV POLUS_EXT=".ome.tif"
-# Change to WARNING for fewer logs, and DEBUG for debugging
-ENV POLUS_LOG="INFO"
-
+ENV EXEC_DIR="/opt/executables"
 ENV POLUS_IMG_EXT=".ome.tif"
 ENV POLUS_TAB_EXT=".csv"
+ENV POLUS_LOG="INFO"
 
 # Work directory defined in the base container
-# WORKDIR ${EXEC_DIR}
+WORKDIR ${EXEC_DIR}
+
+# TODO: Change the tool_dir to the tool directory
+ENV TOOL_DIR="visualization/microjson-to-ome-tool"
 
-COPY pyproject.toml ${EXEC_DIR}
-COPY VERSION ${EXEC_DIR}
-COPY README.md ${EXEC_DIR}
-COPY CHANGELOG.md ${EXEC_DIR}
-COPY src ${EXEC_DIR}/src
+# Copy the repository into the container
+RUN mkdir image-tools
+COPY . ${EXEC_DIR}/image-tools
 
-RUN pip3 install ${EXEC_DIR} --no-cache-dir
+# Install the tool
+RUN pip3 install "${EXEC_DIR}/image-tools/${TOOL_DIR}" --no-cache-dir
 
-# Default command. Additional arguments are provided through the command line
+# Set the entrypoint
+# TODO: Change the entrypoint to the tool entrypoint
 ENTRYPOINT ["python3", "-m", "polus.images.visualization.microjson_to_ome"]
 CMD ["--help"]
diff --git a/visualization/microjson-to-ome-tool/build-docker.sh b/visualization/microjson-to-ome-tool/build-docker.sh
index cea40fddb..01ba8063e 100644
--- a/visualization/microjson-to-ome-tool/build-docker.sh
+++ b/visualization/microjson-to-ome-tool/build-docker.sh
@@ -1,4 +1,23 @@
+
 #!/bin/bash
 
+# Change the name of the tool here
+tool_dir="visualization"
+tool_name="microjson-to-ome-tool"
+
+# The version is read from the VERSION file
 version=$(<VERSION)
-docker build . -t polusai/microjson-to-ome-tool:${version}
+tag="polusai/${tool_name}:${version}"
+echo "Building docker image with tag: ${tag}"
+
+# The current directory and the repository root are saved in variables
+cur_dir=$(pwd)
+repo_root=$(git rev-parse --show-toplevel)
+
+# The Dockerfile and .dockerignore files are copied to the repository root before building the image
+cd ${repo_root}
+cp ./${tool_dir}/${tool_name}/Dockerfile .
+cp .gitingore .dockerignore
+docker build . -t ${tag}
+rm Dockerfile .dockerignore
+cd ${cur_dir}
diff --git a/visualization/ome-to-microjson-tool/Dockerfile b/visualization/ome-to-microjson-tool/Dockerfile
index 37941c5dd..2392645f4 100644
--- a/visualization/ome-to-microjson-tool/Dockerfile
+++ b/visualization/ome-to-microjson-tool/Dockerfile
@@ -9,14 +9,17 @@ ENV POLUS_LOG="INFO"
 # Work directory defined in the base container
 WORKDIR ${EXEC_DIR}
 
-COPY pyproject.toml ${EXEC_DIR}
-COPY VERSION ${EXEC_DIR}
-COPY README.md ${EXEC_DIR}
-COPY CHANGELOG.md ${EXEC_DIR}
-COPY src ${EXEC_DIR}/src
+# TODO: Change the tool_dir to the tool directory
+ENV TOOL_DIR="visualization/ome-to-microjson-tool"
 
-RUN pip3 install ${EXEC_DIR} --no-cache-dir
+# Copy the repository into the container
+RUN mkdir image-tools
+COPY . ${EXEC_DIR}/image-tools
 
-# Default command. Additional arguments are provided through the command line
+# Install the tool
+RUN pip3 install "${EXEC_DIR}/image-tools/${TOOL_DIR}" --no-cache-dir
+
+# Set the entrypoint
+# TODO: Change the entrypoint to the tool entrypoint
 ENTRYPOINT ["python3", "-m", "polus.images.visualization.ome_to_microjson"]
 CMD ["--help"]
diff --git a/visualization/ome-to-microjson-tool/build-docker.sh b/visualization/ome-to-microjson-tool/build-docker.sh
index 016d91348..4a2c9e00e 100755
--- a/visualization/ome-to-microjson-tool/build-docker.sh
+++ b/visualization/ome-to-microjson-tool/build-docker.sh
@@ -1,4 +1,23 @@
+
 #!/bin/bash
 
+# Change the name of the tool here
+tool_dir="visualization"
+tool_name="ome-to-microjson-tool"
+
+# The version is read from the VERSION file
 version=$(<VERSION)
-docker build . -t polusai/ome-to-microjson-tool:${version}
+tag="polusai/${tool_name}:${version}"
+echo "Building docker image with tag: ${tag}"
+
+# The current directory and the repository root are saved in variables
+cur_dir=$(pwd)
+repo_root=$(git rev-parse --show-toplevel)
+
+# The Dockerfile and .dockerignore files are copied to the repository root before building the image
+cd ${repo_root}
+cp ./${tool_dir}/${tool_name}/Dockerfile .
+cp .gitingore .dockerignore
+docker build . -t ${tag}
+rm Dockerfile .dockerignore
+cd ${cur_dir}
diff --git a/visualization/precompute-slide-tool/Dockerfile b/visualization/precompute-slide-tool/Dockerfile
index 3e6515211..31b6e48f4 100644
--- a/visualization/precompute-slide-tool/Dockerfile
+++ b/visualization/precompute-slide-tool/Dockerfile
@@ -1,25 +1,25 @@
 FROM polusai/bfio:2.1.9
 
 # environment variables defined in polusai/bfio
-# ENV EXEC_DIR="/opt/executables"
-# ENV DATA_DIR="/data"
-# ENV POLUS_EXT=".ome.tif"
-# ENV POLUS_LOG="INFO" # Change to WARNING for fewer logs, and DEBUG for debugging
+ENV EXEC_DIR="/opt/executables"
+ENV POLUS_IMG_EXT=".ome.tif"
+ENV POLUS_TAB_EXT=".csv"
+ENV POLUS_LOG="INFO"
 
 # Work directory defined in the base container
-# WORKDIR ${EXEC_DIR}
+WORKDIR ${EXEC_DIR}
 
-COPY pyproject.toml ${EXEC_DIR}
-COPY VERSION ${EXEC_DIR}
-COPY README.md ${EXEC_DIR}
-COPY CHANGELOG.md ${EXEC_DIR}
-COPY src ${EXEC_DIR}/src
+# TODO: Change the tool_dir to the tool directory
+ENV TOOL_DIR="visualization/precompute-slide-tool"
 
-RUN pip3 install ${EXEC_DIR} --no-cache-dir
+# Copy the repository into the container
+RUN mkdir image-tools
+COPY . ${EXEC_DIR}/image-tools
 
-# TODO CHECK if we need this
-RUN python3 -c "import imageio; imageio.plugins.freeimage.download()"
+# Install the tool
+RUN pip3 install "${EXEC_DIR}/image-tools/${TOOL_DIR}" --no-cache-dir
 
-# Default command. Additional arguments are provided through the command line
+# Set the entrypoint
+# TODO: Change the entrypoint to the tool entrypoint
 ENTRYPOINT ["python3", "-m", "polus.images.visualization.precompute_slide"]
 CMD ["--help"]
diff --git a/visualization/precompute-slide-tool/build-docker.sh b/visualization/precompute-slide-tool/build-docker.sh
index 9b67f655b..dc17b16a9 100755
--- a/visualization/precompute-slide-tool/build-docker.sh
+++ b/visualization/precompute-slide-tool/build-docker.sh
@@ -1,14 +1,23 @@
+
 #!/bin/bash
 
-version=$(<VERSION)
-docker build . -t polusai/precompute-slide-tool:${version}
+# Change the name of the tool here
+tool_dir="visualization"
+tool_name="precompute-slide-tool"
 
-# Build for arm using buildx
-# docker buildx build --load --platform linux/arm64/v8 --tag polusai/precompute-slide-tool:${version} .
+# The version is read from the VERSION file
+version=$(<VERSION)
+tag="polusai/${tool_name}:${version}"
+echo "Building docker image with tag: ${tag}"
 
-# Muli-platform deployment for the container (does not work currently)
-# docker buildx build --platform linux/arm64,linux/arm64/v8 --tag polusai/precompute-slide-tool:${version}
+# The current directory and the repository root are saved in variables
+cur_dir=$(pwd)
+repo_root=$(git rev-parse --show-toplevel)
 
-# Muli-platform deployment for the container (does not work currently)
-# docker buildx build --platform linux/arm64,linux/arm64 --tag polusai/precompute-slide-tool:${version} --attest type=provenance,mode=min .
-# docker buildx build --load -t polusai/precompute-slide-tool:${version}  .
+# The Dockerfile and .dockerignore files are copied to the repository root before building the image
+cd ${repo_root}
+cp ./${tool_dir}/${tool_name}/Dockerfile .
+cp .gitingore .dockerignore
+docker build . -t ${tag}
+rm Dockerfile .dockerignore
+cd ${cur_dir}
diff --git a/visualization/tabular-to-microjson-tool/Dockerfile b/visualization/tabular-to-microjson-tool/Dockerfile
index 4b00db308..f8ff1aebd 100644
--- a/visualization/tabular-to-microjson-tool/Dockerfile
+++ b/visualization/tabular-to-microjson-tool/Dockerfile
@@ -1,20 +1,25 @@
-#!/bin/bash
 FROM polusai/bfio:2.1.9
 
 # environment variables defined in polusai/bfio
 ENV EXEC_DIR="/opt/executables"
-ENV POLUS_LOG="INFO"
 ENV POLUS_IMG_EXT=".ome.tif"
 ENV POLUS_TAB_EXT=".csv"
+ENV POLUS_LOG="INFO"
 
 # Work directory defined in the base container
 WORKDIR ${EXEC_DIR}
 
-COPY pyproject.toml ${EXEC_DIR}
-COPY VERSION ${EXEC_DIR}
-COPY README.md ${EXEC_DIR}
-COPY src ${EXEC_DIR}/src
-RUN pip3 install ${EXEC_DIR} --no-cache-dir
+# TODO: Change the tool_dir to the tool directory
+ENV TOOL_DIR="visualization/tabular-to-microjson-tool"
+
+# Copy the repository into the container
+RUN mkdir image-tools
+COPY . ${EXEC_DIR}/image-tools
+
+# Install the tool
+RUN pip3 install "${EXEC_DIR}/image-tools/${TOOL_DIR}" --no-cache-dir
 
+# Set the entrypoint
+# TODO: Change the entrypoint to the tool entrypoint
 ENTRYPOINT ["python3", "-m", "polus.images.visualization.tabular_to_microjson"]
 CMD ["--help"]
diff --git a/visualization/tabular-to-microjson-tool/build-docker.sh b/visualization/tabular-to-microjson-tool/build-docker.sh
index c63f2c211..38e69b219 100644
--- a/visualization/tabular-to-microjson-tool/build-docker.sh
+++ b/visualization/tabular-to-microjson-tool/build-docker.sh
@@ -1,4 +1,23 @@
+
 #!/bin/bash
 
+# Change the name of the tool here
+tool_dir="visualization"
+tool_name="tabular-to-microjson-tool"
+
+# The version is read from the VERSION file
 version=$(<VERSION)
-docker build . -t polusai/tabular-to-microjson-tool:${version}
+tag="polusai/${tool_name}:${version}"
+echo "Building docker image with tag: ${tag}"
+
+# The current directory and the repository root are saved in variables
+cur_dir=$(pwd)
+repo_root=$(git rev-parse --show-toplevel)
+
+# The Dockerfile and .dockerignore files are copied to the repository root before building the image
+cd ${repo_root}
+cp ./${tool_dir}/${tool_name}/Dockerfile .
+cp .gitingore .dockerignore
+docker build . -t ${tag}
+rm Dockerfile .dockerignore
+cd ${cur_dir}