imagej/pyimagej

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Use ImageJ from Python

Stars: 534
Forks: 95
Open beginner issues: 0
Indexed issues: 55

Dominant language: Python
License: No license data
Last GitHub push: Aug 13, 2026
Latest indexed: Sep 17, 2026
Contributing guide: No contributing guide
Code of conduct: No code of conduct
Beginner labels: No beginner labels indexed
PR merge metrics: No merged PRs in 30d

Beginner friendly Everything

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55 open issues indexed

JPype optimization notice Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

imagej/pyimagej#342 · 1 reaction · Opened Aug 14, 2026
Review treatment of `__array__` attribute Open

Difficulty 5/5 Over a week Newbie friendliness 30/100

imagej/pyimagej#341 · Opened May 6, 2026
Failed to create JVM with requested environment Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

imagej/pyimagej#340 · 1 comment · Opened Apr 21, 2026
Forgetting to set JAVA_HOME leads to a somewhat cryptic error message. Open

Difficulty 3/5 1-2 days Newbie friendliness 48/100

imagej/pyimagej#339 · 2 comments · Opened Nov 11, 2025
PyImageJ Documentation Revitalization Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 30/100

imagej/pyimagej#333 · 9 comments · Opened Aug 4, 2025
Add citation info Open

enhancement

Difficulty 2/5 1-3 hours Newbie friendliness 58/100

imagej/pyimagej#332 · Opened Aug 4, 2025
Update documentation on colab installation Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

imagej/pyimagej#331 · Opened Aug 1, 2025
Update instructions and behavior for Fiji-Latest and Java 21 and cjdk Open

enhancement

imagej/pyimagej#329 · 3 reactions · 1 assignee · Opened Jun 24, 2025
Add ij.run_script signature that takes file paths Open

enhancement

imagej/pyimagej#318 · 1 reaction · 1 assignee · Opened Oct 29, 2024
Plugins in the plugin folder cannot be used if they are just .class files. Open

Difficulty 4/5 3-5 days Newbie friendliness 42/100

imagej/pyimagej#313 · 7 comments · Opened Aug 19, 2024
Arguments passed to `run_plugin` replace backslash with forward slash Open

Difficulty 2/5 1-3 hours Newbie friendliness 56/100

imagej/pyimagej#312 · Opened Aug 13, 2024
TypeError: 'NoneType' object is not callable when initializing imagej Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

imagej/pyimagej#308 · 5 comments · Opened Jul 1, 2024
Testing your installation - failed Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

imagej/pyimagej#300 · Opened Mar 3, 2024
Make interactive mode work on macOS Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

imagej/pyimagej#298 · 6 comments · Opened Feb 13, 2024
EXCEPTION_ACCESS_VIOLATION (0xc0000005) Open

tech-support

Difficulty 4/5 3-5 days Newbie friendliness 20/100

imagej/pyimagej#297 · 2 comments · Opened Jan 24, 2024
java.lang.java.lang.NoClassDefFoundError Open

tech-support

Difficulty 4/5 3-5 days Newbie friendliness 30/100

imagej/pyimagej#296 · 11 comments · Opened Jan 12, 2024
Map ImgLib2 ColorTable objects to/from Python cmap.Colormap Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

imagej/pyimagej#294 · Opened Dec 1, 2023
Consider using magicgui for notebook interactivity Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

imagej/pyimagej#293 · Opened Dec 1, 2023
Failed to create a JVM with the requested environment. Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

imagej/pyimagej#291 · 6 comments · Opened Nov 3, 2023
imagej doctor should recognize non-zero return values Open

bug

Difficulty 2/5 1-3 hours Newbie friendliness 48/100

imagej/pyimagej#289 · 1 reaction · Opened Oct 18, 2023
Setting up PyImageJ without internet access Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

imagej/pyimagej#287 · 3 comments · Opened Sep 18, 2023
ImgLabeling conversions use suboptimal tmp directory Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

imagej/pyimagej#286 · Opened Sep 12, 2023
Ij.io().open() raises java.lang.NullPointerException Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

imagej/pyimagej#285 · 4 comments · Opened Sep 11, 2023
Remove warning in upcoming cellpose/stardist segmentation jupyter notebook Open

Difficulty 2/5 1-3 hours Newbie friendliness 50/100

imagej/pyimagej#284 · Opened Sep 6, 2023
Using PyimageJ to collect width by height for individual objects. Open

tech-support

Difficulty 4/5 3-5 days Newbie friendliness 18/100

imagej/pyimagej#274 · 3 comments · Opened Jun 29, 2023
imagej in java code is not regconized Open

tech-support

Difficulty 4/5 3-5 days Newbie friendliness 25/100

imagej/pyimagej#273 · 2 comments · Opened Jun 28, 2023
Multiple copies of verbose output might be shown Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 30/100

imagej/pyimagej#269 · Opened Jun 22, 2023
imagej.doctor should notice subprocess crashes Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 42/100

imagej/pyimagej#268 · Opened Jun 22, 2023
Devise a method for version reproducability Open

enhancement

imagej/pyimagej#263 · 1 assignee · Opened Jun 2, 2023
Support optional installation of pyobjc packages by dependency Open

enhancement macos-gui

Difficulty 2/5 1-3 hours Newbie friendliness 45/100

imagej/pyimagej#262 · 3 comments · Opened May 25, 2023
Add support for `net.imagej.roi.DefultROITree` conversion to Python Open

enhancement

imagej/pyimagej#258 · 1 comment · 1 assignee · Opened Apr 17, 2023
java.lang.RuntimeException: Macro canceled with DiameterJ Segment Open

tech-support

Difficulty 5/5 Over a week Newbie friendliness 25/100

imagej/pyimagej#251 · 5 comments · Opened Feb 20, 2023
Google Colab example in Install.md yields VerifyError Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 35/100

imagej/pyimagej#248 · 5 comments · Opened Feb 2, 2023
Slicing `net.imagej.Dataset` returns an `IntervalView` which does not support dimension metadata Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

imagej/pyimagej#226 · 1 comment · 2 reactions · Opened Oct 4, 2022
Trouble loading TIFF files Open

tech-support

Difficulty 4/5 3-5 days Newbie friendliness 25/100

imagej/pyimagej#218 · 4 comments · Opened Aug 16, 2022
ImageJ Ops threshold results do not work with `3D Object Counter` Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 35/100

imagej/pyimagej#216 · 1 comment · Opened Aug 10, 2022
Indefinite hanging when trying to intialize pyimagej with `ij = imagej.init()` Open

tech-support

Difficulty 4/5 3-5 days Newbie friendliness 28/100

imagej/pyimagej#214 · 2 comments · Opened Aug 5, 2022
Support wrapping a Java-side block of memory allocated off-heap to Python Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 30/100

imagej/pyimagej#203 · 6 comments · Opened May 23, 2022
Support wrapping any arraylike object, which may not be a block of memory, to ImgLib2 Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

imagej/pyimagej#202 · 1 comment · Opened May 23, 2022
[macOS] Initializing PyImageJ before napari breaks napari Open

bug macos-gui

Difficulty 4/5 3-5 days Newbie friendliness 35/100

imagej/pyimagej#197 · 5 comments · Opened Apr 30, 2022
Make ImagePlus subscriptable Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 35/100

imagej/pyimagej#194 · 4 comments · Opened Apr 28, 2022
Add missing unit tests for dims and stack Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 42/100

imagej/pyimagej#190 · Opened Apr 18, 2022
Prune MANIFEST.in Open

question

Difficulty 2/5 1-3 hours Newbie friendliness 45/100

imagej/pyimagej#189 · 5 comments · 1 reaction · Opened Apr 16, 2022
Try setting JAVA_STARTED_ON_FIRST_THREAD_pid environment variable on macOS Open

enhancement macos-gui

imagej/pyimagej#185 · 2 comments · 1 reaction · 1 assignee · Opened Apr 9, 2022
Make a notebook for opening subregions of images Open

enhancement

imagej/pyimagej#171 · 4 comments · 1 assignee · Opened Feb 8, 2022
Passing file-like object to pyimagej Open

question

Difficulty 5/5 Over a week Newbie friendliness 25/100

imagej/pyimagej#156 · 16 comments · Opened Dec 14, 2021
Auto-dispose/cleanup PyImageJ when Python is shutting down Open

bug

imagej/pyimagej#153 · 7 comments · 3 reactions · 1 assignee · Opened Nov 24, 2021
Integrating pyImagej with ImJoy website Open

question

Difficulty 5/5 Over a week Newbie friendliness 25/100

imagej/pyimagej#147 · 10 comments · Opened Nov 1, 2021
Integrate stubgenj somehow Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

imagej/pyimagej#145 · 1 comment · Opened Oct 21, 2021
Expand directory-based initialization options Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

imagej/pyimagej#142 · 1 comment · 1 reaction · Opened Oct 1, 2021

imagej/pyimagej

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