├── .github ├── scripts │ └── update_notebook.py ├── templates │ ├── personalize_gemini_cell.py.j2 │ └── set_coding_rules_cell.py.j2 └── workflows │ ├── build.yml │ ├── check-wip-commits.yml │ └── update-notebook.yml ├── .gitignore ├── .mailmap ├── .pre-commit-config.yaml ├── .readthedocs.yaml ├── LICENSE.txt ├── MANIFEST.in ├── Makefile ├── README.md ├── bin ├── check.sh ├── clean.sh ├── lint.sh └── test.sh ├── conftest.py ├── doc ├── 01-Starting-PyImageJ.ipynb ├── 02-Working-with-Java-classes-and-Python.ipynb ├── 03-Sending-Data-to-Java.ipynb ├── 04-Retrieving-Data-from-Java.ipynb ├── 05-Convenience-methods-of-PyImageJ.ipynb ├── 06-Working-with-Images.ipynb ├── 07-Running-Macros-Scripts-and-Plugins.ipynb ├── 08-Discover-and-run-ImageJ-commands.ipynb ├── 09-Working-with-Large-Images.ipynb ├── 10-Using-ImageJ-Ops.ipynb ├── 11-Working-with-the-original-ImageJ.ipynb ├── 12-Troubleshooting.ipynb ├── AI-Tutorial-Notebook.md ├── Cellpose-StarDist-Segmentation.ipynb ├── Citation.rst ├── Classic-Segmentation.ipynb ├── Deconvolution.ipynb ├── Development.md ├── GLCM.ipynb ├── Google-Colab-Basics.md ├── Headless.md ├── Initialization.md ├── Install.md ├── Makefile ├── Prompt-Engineering.md ├── Puncta-Segmentation.ipynb ├── README.md ├── Troubleshooting.md ├── api.rst ├── cellprofiler │ ├── MakeBBBC030GT_ManuallyFix.cppipe │ ├── README.md │ ├── RunImageJMacroWorkflow │ │ ├── RunImageJBallWithMacro.cppipe │ │ └── test_ball_macro.py │ ├── RunImageJScriptRollingBall │ │ ├── RunImageJBall.cppipe │ │ └── test_ball.bsh │ ├── RunImageJScriptSegmentation │ │ ├── RunImageJScriptSegmentation_withGT.cppipe │ │ ├── classifier.model │ │ └── test.bsh │ └── figure.svg ├── conf.py ├── doc-images │ ├── accept-and-run.jpg │ ├── add-files.jpg │ ├── chat-toggle.jpg │ ├── code-menu.jpg │ ├── colab-persona.jpg │ ├── colab-ui.jpg │ ├── colab-warning.jpg │ ├── copy-ai-text.jpg │ ├── explain-error.jpg │ ├── file-sidebar.jpg │ ├── imagej_ui_macro_recorder.png │ ├── logo.svg │ ├── macro_recorder_find_maxima.png │ ├── nb-collapsed.jpg │ ├── nb-hide-output.jpg │ ├── nb-progress.jpg │ ├── nb-run-all.jpg │ ├── nb-show-code.png │ ├── nb-start-coding.jpg │ ├── nb-troubleshoot.jpg │ ├── new-cells.jpg │ ├── open-notebooks.jpg │ ├── run-cell.jpg │ ├── runtime-connected.jpg │ ├── runtime-dropdown.jpg │ ├── settings-1.jpg │ ├── settings-2.jpg │ ├── task-running.jpg │ ├── test_still_analyze_particles.png │ └── test_still_find_maxima.png ├── examples │ ├── README.md │ ├── blob_detection_interactive.py │ ├── blob_detection_xvfb.py │ ├── blob_interactive.rst │ └── blob_xvfb.rst ├── imagej-ops-use-cases.rst ├── index.rst ├── integration-use-cases.rst ├── llms │ ├── README.md │ ├── custom-pyimagej-ai-guide.ipynb │ ├── personas │ │ ├── activities │ │ │ ├── base_activity.md │ │ │ ├── coding_advanced.md │ │ │ ├── coding_beginner.md │ │ │ ├── coding_intermediate.md │ │ │ ├── colab_advanced.md │ │ │ ├── colab_beginner.md │ │ │ ├── colab_intermediate.md │ │ │ ├── pyimagej_advanced.md │ │ │ ├── pyimagej_beginner.md │ │ │ └── pyimagej_intermediate.md │ │ └── base_persona.md │ ├── pyimagej-ai-guide.ipynb │ └── rulesets │ │ ├── environments │ │ ├── env_colab.md │ │ ├── env_headless.md │ │ ├── env_interactive.md │ │ └── env_scripting.md │ │ ├── imagej1_api.md │ │ ├── imagej_ops.md │ │ └── pyimagej_core.md ├── make.bat ├── notebooks.rst ├── other_use_cases.rst ├── sample-data │ ├── test_image.tif │ ├── test_still.tif │ ├── test_still_stack.tif │ └── test_timeseries.tif └── segmentation-use-cases.rst ├── environment.yml ├── pyproject.toml ├── src └── imagej │ ├── __init__.py │ ├── _java.py │ ├── convert.py │ ├── dims.py │ ├── doctor.py │ ├── images.py │ └── stack.py └── tests ├── test_callbacks.py ├── test_ctypes.py ├── test_doctor.py ├── test_fiji.py ├── test_image_conversion.py ├── test_labeling.py ├── test_legacy.py ├── test_macros_scripts.py ├── test_ops.py └── test_rai_arraylike.py /.github/scripts/update_notebook.py: 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