updated dependencies & added CLT & ICT

segmentation/kaggle-nuclei-segmentation-tool/.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.1.5-dev1
+current_version = 0.1.5-dev2
 commit = False
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<dev>\d+))?

segmentation/kaggle-nuclei-segmentation-tool/CHANGELOG.md

@@ -3,3 +3,9 @@
 ## 0.1.5-dev1
 
 Initial release.
+
+## 0.1.5-dev2
+
+Updated the bfio package.
+Pinned the TensorFlow version.
+Created ICT and CLT for this plugin.

segmentation/kaggle-nuclei-segmentation-tool/Dockerfile

@@ -1,4 +1,4 @@
-FROM polusai/bfio:2.1.9
+FROM polusai/bfio:2.4.4
 
 # environment variables defined in polusai/bfio
 ENV EXEC_DIR="/opt/executables"

segmentation/kaggle-nuclei-segmentation-tool/KaggleNucleiSegmentation.cwl

@@ -0,0 +1,32 @@
+class: CommandLineTool
+cwlVersion: v1.2
+inputs:
+  filePattern:
+    inputBinding:
+      prefix: --filePattern
+    type: string?
+  inpDir:
+    inputBinding:
+      prefix: --inpDir
+    type: Directory
+  outDir:
+    inputBinding:
+      prefix: --outDir
+    type: Directory
+  preview:
+    inputBinding:
+      prefix: --preview
+    type: boolean?
+outputs:
+  outDir:
+    outputBinding:
+      glob: $(inputs.outDir.basename)
+    type: Directory
+requirements:
+  DockerRequirement:
+    dockerPull: polusai/kaggle-nuclei-segmentation-tool:0.1.5-dev2
+  InitialWorkDirRequirement:
+    listing:
+    - entry: $(inputs.outDir)
+      writable: true
+  InlineJavascriptRequirement: {}

segmentation/kaggle-nuclei-segmentation-tool/README.md

@@ -1,4 +1,4 @@
-# Kaggle Nuclei Segmentation (v0.1.5-dev1)
+# Kaggle Nuclei Segmentation (v0.1.5-dev2)
 
 Segments cell nuclei using U-Net in Tensorflow.
 

segmentation/kaggle-nuclei-segmentation-tool/VERSION

@@ -1 +1 @@
-0.1.5-dev1
+0.1.5-dev2

segmentation/kaggle-nuclei-segmentation-tool/ict.yaml

@@ -0,0 +1,54 @@
+author:
+- Gauhar Bains
+- Konstantin Taletskiy
+- Nick Schaub
+- Hamdah Shafqat
+contact: [email protected]
+container: polusai/kaggle-nuclei-segmentation-tool:0.1.5-dev2
+description: Segments cell nuclei using U-Net in Tensorflow. Neural net architecture
+  and pretrained weights are taken from Data Science Bowl 2018 entry by Muhammad Asim
+entrypoint: python3 -m polus.images.segmentation.kaggle_nuclei_segmentation
+inputs:
+- description: Input image collection to be processed by this plugin
+  format:
+  - collection
+  name: inpDir
+  required: true
+  type: path
+- description: Filename pattern used to separate data
+  format:
+  - string
+  name: filePattern
+  required: false
+  type: string
+- description: Generate an output preview.
+  format:
+  - boolean
+  name: preview
+  required: false
+  type: boolean
+name: polusai/KaggleNucleiSegmentation
+outputs:
+- description: Output collection
+  format:
+  - collection
+  name: outDir
+  required: true
+  type: path
+repository: https://github.com/PolusAI/image-tools
+specVersion: 1.0.0
+title: Kaggle Nuclei Segmentation
+ui:
+- description: Input image collection to be processed by this plugin
+  key: inputs.inpDir
+  title: Input collection
+  type: path
+- description: Filename pattern used to separate data
+  key: inputs.filePattern
+  title: Filename pattern
+  type: text
+- description: Generate an output preview.
+  key: inputs.preview
+  title: preview
+  type: checkbox
+version: 0.1.5-dev2

segmentation/kaggle-nuclei-segmentation-tool/plugin.json

@@ -1,14 +1,14 @@
 {
   "name": "Kaggle Nuclei Segmentation",
-  "version": "0.1.5-dev1",
+  "version": "0.1.5-dev2",
   "title": "Kaggle Nuclei Segmentation",
   "description": "Segments cell nuclei using U-Net in Tensorflow. Neural net architecture and pretrained weights are taken from Data Science Bowl 2018 entry by Muhammad Asim",
-  "author": "Gauhar Bains,  Konstantin Taletskiy,Nick Schaub , Hamdah Shafqat Abbasi ([email protected], [email protected], [email protected], [email protected])",
+  "author": "Gauhar Bains ([email protected]),  Konstantin Taletskiy (Konstantin[email protected]), Nick Schaub ([email protected]) , Hamdah Shafqat Abbasi ([email protected])",
   "institution": "National Center for Advancing Translational Sciences, National Institutes of Health",
   "repository": "https://github.com/PolusAI/image-tools",
   "website": "https://ncats.nih.gov/preclinical/core/informatics",
   "citation": "",
-  "containerId": "polusai/kaggle-nuclei-segmentation-tool:0.1.5-dev1",
+  "containerId": "polusai/kaggle-nuclei-segmentation-tool:0.1.5-dev2",
   "baseCommand": [
     "python3",
     "-m",

segmentation/kaggle-nuclei-segmentation-tool/pyproject.toml

@@ -1,18 +1,19 @@
 [tool.poetry]
 name = "polus-images-segmentation-kaggle-nuclei-segmentation"
-version = "0.1.5-dev1"
+version = "0.1.5-dev2"
 description = "Segments cell nuclei using U-Net in Tensorflow. Neural net architecture and pretrained weights are taken from Data Science Bowl 2018 entry by Muhammad Asim"
 authors = ["Gauhar Bains,  Konstantin Taletskiy,Nick Schaub , Hamdah Shafqat Abbasi <[email protected], [email protected], [email protected], [email protected]>"]
 readme = "README.md"
 packages = [{include = "polus", from = "src"}]
 
 [tool.poetry.dependencies]
 python = ">=3.9,<3.12"
-bfio = {version = "2.1.9", extras = ["all"]}
+bfio = {version = "^2.4.4", extras = ["all"]}
 filepattern = ">=2.0.4,<3.0"
 typer = "^0.7.0"
-tensorflow = "^2.15.0"
+tensorflow = "2.15.0"
 opencv-python-headless = "^4.9.0.80"
+numpy ="<2.0.0"
 
 [tool.poetry.group.dev.dependencies]
 bump2version = "^1.0.1"

segmentation/kaggle-nuclei-segmentation-tool/src/polus/images/segmentation/kaggle_nuclei_segmentation/__init__.py

@@ -1,3 +1,3 @@
 """Kaggle Nuclei Segmentation."""
 
-__version__ = "0.1.5-dev"
+__version__ = "0.1.5-dev2"