From e84bec6ed3b24c53aabb45742058cddb26bbe025 Mon Sep 17 00:00:00 2001
From: Najib Ishaq <najib_ishaq@zoho.com>
Date: Fri, 28 Jun 2024 11:25:58 -0400
Subject: [PATCH] fix: installing iamgej in dockerfiles

---
 clustering/k-means-clustering-tool/Dockerfile                   | 1 +
 clustering/outlier-removal-tool/Dockerfile                      | 1 +
 features/feature-segmentation-eval-tool/Dockerfile              | 1 +
 features/nyxus-tool/Dockerfile                                  | 1 +
 features/pixel-segmentation-eval-tool/Dockerfile                | 1 +
 features/region-segmentation-eval-tool/Dockerfile               | 1 +
 formats/arrow-to-tabular-tool/Dockerfile                        | 1 +
 formats/file-renaming-tool/Dockerfile                           | 1 +
 formats/label-to-vector-tool/Dockerfile                         | 1 +
 formats/ome-converter-tool/Dockerfile                           | 1 +
 formats/tabular-converter-tool/Dockerfile                       | 1 +
 formats/tabular-to-arrow-tool/Dockerfile                        | 1 +
 formats/vector-to-label-tool/Dockerfile                         | 1 +
 regression/basic-flatfield-estimation-tool/Dockerfile           | 1 +
 regression/theia-bleedthrough-estimation-tool/Dockerfile        | 1 +
 segmentation/cell-border-segmentation-tool/Dockerfile           | 1 +
 segmentation/mesmer-inference-tool/Dockerfile                   | 1 +
 segmentation/mesmer-training-tool/Dockerfile                    | 1 +
 transforms/images/apply-flatfield-tool/Dockerfile               | 1 +
 transforms/images/binary-operations-tool/Dockerfile             | 1 +
 transforms/images/image-assembler-tool/Dockerfile               | 1 +
 transforms/images/image-calculator-tool/Dockerfile              | 1 +
 transforms/images/lumos-bleedthrough-correction-tool/Dockerfile | 1 +
 transforms/images/montage-tool/Dockerfile                       | 1 +
 transforms/images/roi-relabel-tool/Dockerfile                   | 1 +
 transforms/tabular/tabular-thresholding-tool/Dockerfile         | 1 +
 utils/rxiv-download-tool/Dockerfile                             | 1 +
 visualization/microjson-to-ome-tool/Dockerfile                  | 1 +
 visualization/ome-to-microjson-tool/Dockerfile                  | 1 +
 visualization/precompute-slide-tool/Dockerfile                  | 1 +
 visualization/tabular-to-microjson-tool/Dockerfile              | 1 +
 31 files changed, 31 insertions(+)

diff --git a/clustering/k-means-clustering-tool/Dockerfile b/clustering/k-means-clustering-tool/Dockerfile
index 5a574c825..166e3982f 100644
--- a/clustering/k-means-clustering-tool/Dockerfile
+++ b/clustering/k-means-clustering-tool/Dockerfile
@@ -10,6 +10,7 @@ ENV POLUS_LOG="INFO"
 WORKDIR ${EXEC_DIR}
 
 # Initialize ImageJ
+pip3 install pyimagej==1.4.1 jpype1==1.5.0 scyjava==1.9.1 imglyb==2.1.0
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
 # TODO: Change the tool_dir to the tool directory
diff --git a/clustering/outlier-removal-tool/Dockerfile b/clustering/outlier-removal-tool/Dockerfile
index 4749a6d0b..91bebfd8e 100644
--- a/clustering/outlier-removal-tool/Dockerfile
+++ b/clustering/outlier-removal-tool/Dockerfile
@@ -10,6 +10,7 @@ ENV POLUS_LOG="INFO"
 WORKDIR ${EXEC_DIR}
 
 # Initialize ImageJ
+pip3 install pyimagej==1.4.1 jpype1==1.5.0 scyjava==1.9.1 imglyb==2.1.0
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
 # TODO: Change the tool_dir to the tool directory
diff --git a/features/feature-segmentation-eval-tool/Dockerfile b/features/feature-segmentation-eval-tool/Dockerfile
index c32cd1c1e..c477b536d 100644
--- a/features/feature-segmentation-eval-tool/Dockerfile
+++ b/features/feature-segmentation-eval-tool/Dockerfile
@@ -10,6 +10,7 @@ ENV POLUS_LOG="INFO"
 WORKDIR ${EXEC_DIR}
 
 # Initialize ImageJ
+pip3 install pyimagej==1.4.1 jpype1==1.5.0 scyjava==1.9.1 imglyb==2.1.0
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
 # TODO: Change the tool_dir to the tool directory
diff --git a/features/nyxus-tool/Dockerfile b/features/nyxus-tool/Dockerfile
index 542218cc7..289f71b0f 100755
--- a/features/nyxus-tool/Dockerfile
+++ b/features/nyxus-tool/Dockerfile
@@ -10,6 +10,7 @@ ENV POLUS_LOG="INFO"
 WORKDIR ${EXEC_DIR}
 
 # Initialize ImageJ
+pip3 install pyimagej==1.4.1 jpype1==1.5.0 scyjava==1.9.1 imglyb==2.1.0
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
 # TODO: Change the tool_dir to the tool directory
diff --git a/features/pixel-segmentation-eval-tool/Dockerfile b/features/pixel-segmentation-eval-tool/Dockerfile
index 6abe61c46..ead5f65e3 100644
--- a/features/pixel-segmentation-eval-tool/Dockerfile
+++ b/features/pixel-segmentation-eval-tool/Dockerfile
@@ -10,6 +10,7 @@ ENV POLUS_LOG="INFO"
 WORKDIR ${EXEC_DIR}
 
 # Initialize ImageJ
+pip3 install pyimagej==1.4.1 jpype1==1.5.0 scyjava==1.9.1 imglyb==2.1.0
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
 # TODO: Change the tool_dir to the tool directory
diff --git a/features/region-segmentation-eval-tool/Dockerfile b/features/region-segmentation-eval-tool/Dockerfile
index 10c2a742e..d1112c509 100644
--- a/features/region-segmentation-eval-tool/Dockerfile
+++ b/features/region-segmentation-eval-tool/Dockerfile
@@ -10,6 +10,7 @@ ENV POLUS_LOG="INFO"
 WORKDIR ${EXEC_DIR}
 
 # Initialize ImageJ
+pip3 install pyimagej==1.4.1 jpype1==1.5.0 scyjava==1.9.1 imglyb==2.1.0
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
 # TODO: Change the tool_dir to the tool directory
diff --git a/formats/arrow-to-tabular-tool/Dockerfile b/formats/arrow-to-tabular-tool/Dockerfile
index da9d9cf92..b5fcb5bcd 100644
--- a/formats/arrow-to-tabular-tool/Dockerfile
+++ b/formats/arrow-to-tabular-tool/Dockerfile
@@ -10,6 +10,7 @@ ENV POLUS_LOG="INFO"
 WORKDIR ${EXEC_DIR}
 
 # Initialize ImageJ
+pip3 install pyimagej==1.4.1 jpype1==1.5.0 scyjava==1.9.1 imglyb==2.1.0
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
 # TODO: Change the tool_dir to the tool directory
diff --git a/formats/file-renaming-tool/Dockerfile b/formats/file-renaming-tool/Dockerfile
index f9731d1fe..6da79e00e 100644
--- a/formats/file-renaming-tool/Dockerfile
+++ b/formats/file-renaming-tool/Dockerfile
@@ -10,6 +10,7 @@ ENV POLUS_LOG="INFO"
 WORKDIR ${EXEC_DIR}
 
 # Initialize ImageJ
+pip3 install pyimagej==1.4.1 jpype1==1.5.0 scyjava==1.9.1 imglyb==2.1.0
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
 # TODO: Change the tool_dir to the tool directory
diff --git a/formats/label-to-vector-tool/Dockerfile b/formats/label-to-vector-tool/Dockerfile
index 1ff791d10..feaab4626 100644
--- a/formats/label-to-vector-tool/Dockerfile
+++ b/formats/label-to-vector-tool/Dockerfile
@@ -10,6 +10,7 @@ ENV POLUS_LOG="INFO"
 WORKDIR ${EXEC_DIR}
 
 # Initialize ImageJ
+pip3 install pyimagej==1.4.1 jpype1==1.5.0 scyjava==1.9.1 imglyb==2.1.0
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
 # TODO: Change the tool_dir to the tool directory
diff --git a/formats/ome-converter-tool/Dockerfile b/formats/ome-converter-tool/Dockerfile
index 406eb3777..3997f4d39 100644
--- a/formats/ome-converter-tool/Dockerfile
+++ b/formats/ome-converter-tool/Dockerfile
@@ -10,6 +10,7 @@ ENV POLUS_LOG="INFO"
 WORKDIR ${EXEC_DIR}
 
 # Initialize ImageJ
+pip3 install pyimagej==1.4.1 jpype1==1.5.0 scyjava==1.9.1 imglyb==2.1.0
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
 # TODO: Change the tool_dir to the tool directory
diff --git a/formats/tabular-converter-tool/Dockerfile b/formats/tabular-converter-tool/Dockerfile
index 862451184..b99d1190a 100644
--- a/formats/tabular-converter-tool/Dockerfile
+++ b/formats/tabular-converter-tool/Dockerfile
@@ -10,6 +10,7 @@ ENV POLUS_LOG="INFO"
 WORKDIR ${EXEC_DIR}
 
 # Initialize ImageJ
+pip3 install pyimagej==1.4.1 jpype1==1.5.0 scyjava==1.9.1 imglyb==2.1.0
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
 # TODO: Change the tool_dir to the tool directory
diff --git a/formats/tabular-to-arrow-tool/Dockerfile b/formats/tabular-to-arrow-tool/Dockerfile
index a323bb704..9d469ebfc 100644
--- a/formats/tabular-to-arrow-tool/Dockerfile
+++ b/formats/tabular-to-arrow-tool/Dockerfile
@@ -10,6 +10,7 @@ ENV POLUS_LOG="INFO"
 WORKDIR ${EXEC_DIR}
 
 # Initialize ImageJ
+pip3 install pyimagej==1.4.1 jpype1==1.5.0 scyjava==1.9.1 imglyb==2.1.0
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
 # TODO: Change the tool_dir to the tool directory
diff --git a/formats/vector-to-label-tool/Dockerfile b/formats/vector-to-label-tool/Dockerfile
index a6a95e83c..2e01c3258 100644
--- a/formats/vector-to-label-tool/Dockerfile
+++ b/formats/vector-to-label-tool/Dockerfile
@@ -10,6 +10,7 @@ ENV POLUS_LOG="INFO"
 WORKDIR ${EXEC_DIR}
 
 # Initialize ImageJ
+pip3 install pyimagej==1.4.1 jpype1==1.5.0 scyjava==1.9.1 imglyb==2.1.0
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
 # TODO: Change the tool_dir to the tool directory
diff --git a/regression/basic-flatfield-estimation-tool/Dockerfile b/regression/basic-flatfield-estimation-tool/Dockerfile
index 8b44bb626..0145a131e 100644
--- a/regression/basic-flatfield-estimation-tool/Dockerfile
+++ b/regression/basic-flatfield-estimation-tool/Dockerfile
@@ -40,6 +40,7 @@ ENV DATA_DIR="/data"
 WORKDIR ${EXEC_DIR}
 
 # Initialize ImageJ
+pip3 install pyimagej==1.4.1 jpype1==1.5.0 scyjava==1.9.1 imglyb==2.1.0
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
 # TODO: Change the tool_dir to the tool directory
diff --git a/regression/theia-bleedthrough-estimation-tool/Dockerfile b/regression/theia-bleedthrough-estimation-tool/Dockerfile
index c35b918bb..837420ddb 100644
--- a/regression/theia-bleedthrough-estimation-tool/Dockerfile
+++ b/regression/theia-bleedthrough-estimation-tool/Dockerfile
@@ -39,6 +39,7 @@ ENV DATA_DIR="/data"
 # Work directory defined in the base container
 WORKDIR ${EXEC_DIR}# Initialize ImageJ
 
+pip3 install pyimagej==1.4.1 jpype1==1.5.0 scyjava==1.9.1 imglyb==2.1.0
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
 # TODO: Change the tool_dir to the tool directory
diff --git a/segmentation/cell-border-segmentation-tool/Dockerfile b/segmentation/cell-border-segmentation-tool/Dockerfile
index 765b8e4d3..5494aba89 100644
--- a/segmentation/cell-border-segmentation-tool/Dockerfile
+++ b/segmentation/cell-border-segmentation-tool/Dockerfile
@@ -10,6 +10,7 @@ ENV POLUS_LOG="INFO"
 WORKDIR ${EXEC_DIR}
 
 # Initialize ImageJ
+pip3 install pyimagej==1.4.1 jpype1==1.5.0 scyjava==1.9.1 imglyb==2.1.0
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
 # TODO: Change the tool_dir to the tool directory
diff --git a/segmentation/mesmer-inference-tool/Dockerfile b/segmentation/mesmer-inference-tool/Dockerfile
index c3228fd2d..535694249 100644
--- a/segmentation/mesmer-inference-tool/Dockerfile
+++ b/segmentation/mesmer-inference-tool/Dockerfile
@@ -23,6 +23,7 @@ RUN ln -sf /usr/bin/python3.9 /usr/bin/python3
 WORKDIR ${EXEC_DIR}
 
 # Initialize ImageJ
+pip3 install pyimagej==1.4.1 jpype1==1.5.0 scyjava==1.9.1 imglyb==2.1.0
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
 # TODO: Change the tool_dir to the tool directory
diff --git a/segmentation/mesmer-training-tool/Dockerfile b/segmentation/mesmer-training-tool/Dockerfile
index 6f88131bf..87e2fd195 100644
--- a/segmentation/mesmer-training-tool/Dockerfile
+++ b/segmentation/mesmer-training-tool/Dockerfile
@@ -23,6 +23,7 @@ RUN ln -sf /usr/bin/python3.9 /usr/bin/python3
 WORKDIR ${EXEC_DIR}
 
 # Initialize ImageJ
+pip3 install pyimagej==1.4.1 jpype1==1.5.0 scyjava==1.9.1 imglyb==2.1.0
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
 # TODO: Change the tool_dir to the tool directory
diff --git a/transforms/images/apply-flatfield-tool/Dockerfile b/transforms/images/apply-flatfield-tool/Dockerfile
index b25340945..4b5ee1c0c 100644
--- a/transforms/images/apply-flatfield-tool/Dockerfile
+++ b/transforms/images/apply-flatfield-tool/Dockerfile
@@ -10,6 +10,7 @@ ENV POLUS_LOG="INFO"
 WORKDIR ${EXEC_DIR}
 
 # Initialize ImageJ
+pip3 install pyimagej==1.4.1 jpype1==1.5.0 scyjava==1.9.1 imglyb==2.1.0
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
 # TODO: Change the tool_dir to the tool directory
diff --git a/transforms/images/binary-operations-tool/Dockerfile b/transforms/images/binary-operations-tool/Dockerfile
index 08658333c..499dcd2a4 100644
--- a/transforms/images/binary-operations-tool/Dockerfile
+++ b/transforms/images/binary-operations-tool/Dockerfile
@@ -10,6 +10,7 @@ ENV POLUS_LOG="INFO"
 WORKDIR ${EXEC_DIR}
 
 # Initialize ImageJ
+pip3 install pyimagej==1.4.1 jpype1==1.5.0 scyjava==1.9.1 imglyb==2.1.0
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
 # TODO: Change the tool_dir to the tool directory
diff --git a/transforms/images/image-assembler-tool/Dockerfile b/transforms/images/image-assembler-tool/Dockerfile
index fdd7855f3..dc68a5b46 100644
--- a/transforms/images/image-assembler-tool/Dockerfile
+++ b/transforms/images/image-assembler-tool/Dockerfile
@@ -10,6 +10,7 @@ ENV POLUS_LOG="INFO"
 WORKDIR ${EXEC_DIR}
 
 # Initialize ImageJ
+pip3 install pyimagej==1.4.1 jpype1==1.5.0 scyjava==1.9.1 imglyb==2.1.0
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
 # TODO: Change the tool_dir to the tool directory
diff --git a/transforms/images/image-calculator-tool/Dockerfile b/transforms/images/image-calculator-tool/Dockerfile
index 4af9b2564..18e922409 100644
--- a/transforms/images/image-calculator-tool/Dockerfile
+++ b/transforms/images/image-calculator-tool/Dockerfile
@@ -10,6 +10,7 @@ ENV POLUS_LOG="INFO"
 WORKDIR ${EXEC_DIR}
 
 # Initialize ImageJ
+pip3 install pyimagej==1.4.1 jpype1==1.5.0 scyjava==1.9.1 imglyb==2.1.0
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
 # TODO: Change the tool_dir to the tool directory
diff --git a/transforms/images/lumos-bleedthrough-correction-tool/Dockerfile b/transforms/images/lumos-bleedthrough-correction-tool/Dockerfile
index 2f12553de..859ee9e41 100644
--- a/transforms/images/lumos-bleedthrough-correction-tool/Dockerfile
+++ b/transforms/images/lumos-bleedthrough-correction-tool/Dockerfile
@@ -10,6 +10,7 @@ ENV POLUS_LOG="INFO"
 WORKDIR ${EXEC_DIR}
 
 # Initialize ImageJ
+pip3 install pyimagej==1.4.1 jpype1==1.5.0 scyjava==1.9.1 imglyb==2.1.0
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
 # TODO: Change the tool_dir to the tool directory
diff --git a/transforms/images/montage-tool/Dockerfile b/transforms/images/montage-tool/Dockerfile
index 006abffbd..6dafc0b5d 100644
--- a/transforms/images/montage-tool/Dockerfile
+++ b/transforms/images/montage-tool/Dockerfile
@@ -10,6 +10,7 @@ ENV POLUS_LOG="INFO"
 WORKDIR ${EXEC_DIR}
 
 # Initialize ImageJ
+pip3 install pyimagej==1.4.1 jpype1==1.5.0 scyjava==1.9.1 imglyb==2.1.0
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
 # TODO: Change the tool_dir to the tool directory
diff --git a/transforms/images/roi-relabel-tool/Dockerfile b/transforms/images/roi-relabel-tool/Dockerfile
index 7694421a0..34a78c1b1 100644
--- a/transforms/images/roi-relabel-tool/Dockerfile
+++ b/transforms/images/roi-relabel-tool/Dockerfile
@@ -10,6 +10,7 @@ ENV POLUS_LOG="INFO"
 WORKDIR ${EXEC_DIR}
 
 # Initialize ImageJ
+pip3 install pyimagej==1.4.1 jpype1==1.5.0 scyjava==1.9.1 imglyb==2.1.0
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
 # TODO: Change the tool_dir to the tool directory
diff --git a/transforms/tabular/tabular-thresholding-tool/Dockerfile b/transforms/tabular/tabular-thresholding-tool/Dockerfile
index b6cdb4ab8..e2ef50594 100644
--- a/transforms/tabular/tabular-thresholding-tool/Dockerfile
+++ b/transforms/tabular/tabular-thresholding-tool/Dockerfile
@@ -10,6 +10,7 @@ ENV POLUS_LOG="INFO"
 WORKDIR ${EXEC_DIR}
 
 # Initialize ImageJ
+pip3 install pyimagej==1.4.1 jpype1==1.5.0 scyjava==1.9.1 imglyb==2.1.0
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
 # TODO: Change the tool_dir to the tool directory
diff --git a/utils/rxiv-download-tool/Dockerfile b/utils/rxiv-download-tool/Dockerfile
index 6bf7ff49a..a1f41ac04 100644
--- a/utils/rxiv-download-tool/Dockerfile
+++ b/utils/rxiv-download-tool/Dockerfile
@@ -10,6 +10,7 @@ ENV POLUS_LOG="INFO"
 WORKDIR ${EXEC_DIR}
 
 # Initialize ImageJ
+pip3 install pyimagej==1.4.1 jpype1==1.5.0 scyjava==1.9.1 imglyb==2.1.0
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
 # TODO: Change the tool_dir to the tool directory
diff --git a/visualization/microjson-to-ome-tool/Dockerfile b/visualization/microjson-to-ome-tool/Dockerfile
index 9482fb9b1..cb2975a3e 100644
--- a/visualization/microjson-to-ome-tool/Dockerfile
+++ b/visualization/microjson-to-ome-tool/Dockerfile
@@ -10,6 +10,7 @@ ENV POLUS_LOG="INFO"
 WORKDIR ${EXEC_DIR}
 
 # Initialize ImageJ
+pip3 install pyimagej==1.4.1 jpype1==1.5.0 scyjava==1.9.1 imglyb==2.1.0
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
 # TODO: Change the tool_dir to the tool directory
diff --git a/visualization/ome-to-microjson-tool/Dockerfile b/visualization/ome-to-microjson-tool/Dockerfile
index ecbf5cfc2..b6737f1c6 100644
--- a/visualization/ome-to-microjson-tool/Dockerfile
+++ b/visualization/ome-to-microjson-tool/Dockerfile
@@ -10,6 +10,7 @@ ENV POLUS_LOG="INFO"
 WORKDIR ${EXEC_DIR}
 
 # Initialize ImageJ
+pip3 install pyimagej==1.4.1 jpype1==1.5.0 scyjava==1.9.1 imglyb==2.1.0
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
 # TODO: Change the tool_dir to the tool directory
diff --git a/visualization/precompute-slide-tool/Dockerfile b/visualization/precompute-slide-tool/Dockerfile
index b5889b0f1..e5dc1cfc0 100644
--- a/visualization/precompute-slide-tool/Dockerfile
+++ b/visualization/precompute-slide-tool/Dockerfile
@@ -10,6 +10,7 @@ ENV POLUS_LOG="INFO"
 WORKDIR ${EXEC_DIR}
 
 # Initialize ImageJ
+pip3 install pyimagej==1.4.1 jpype1==1.5.0 scyjava==1.9.1 imglyb==2.1.0
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
 # TODO: Change the tool_dir to the tool directory
diff --git a/visualization/tabular-to-microjson-tool/Dockerfile b/visualization/tabular-to-microjson-tool/Dockerfile
index 49eb0fc43..10529ce8f 100644
--- a/visualization/tabular-to-microjson-tool/Dockerfile
+++ b/visualization/tabular-to-microjson-tool/Dockerfile
@@ -10,6 +10,7 @@ ENV POLUS_LOG="INFO"
 WORKDIR ${EXEC_DIR}
 
 # Initialize ImageJ
+pip3 install pyimagej==1.4.1 jpype1==1.5.0 scyjava==1.9.1 imglyb==2.1.0
 RUN python3 -c "import imagej; imagej.init('sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4')"
 
 # TODO: Change the tool_dir to the tool directory