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imagej

36 indexed repositories · View on GitHub

imagej2
Open scientific N-dimensional image processing :microscope: :sparkler:

Java · 1405 stars
ImageJ
Public domain software for processing and analyzing scientific images

Java · 786 stars
pyimagej
Use ImageJ from Python

Python · 534 stars
tutorials
ImageJ2 programming examples

Jupyter Notebook · 200 stars
imagej-ops
ImageJ Ops: "Write once, run anywhere" image processing

Java · 94 stars
imagej-server
A RESTful web server for ImageJ [EXPERIMENTAL]

Java · 40 stars
example-imagej2-command
Simple Maven project for an ImageJ2 command

Java · 35 stars
example-legacy-plugin
Simple Maven project for an ImageJ 1.x plugin

Java · 35 stars
napari-imagej
Use ImageJ functionality from napari

Python · 34 stars
imagej.github.io
The ImageJ wiki

JavaScript · 30 stars
imagej-scripting
ImageJ-specific applications of the SciJava script languages

Python · 27 stars
imagej-tensorflow
ImageJ/TensorFlow integration library

Java · 26 stars
imagej-launcher
The ImageJ native launcher

Java · 24 stars
imagej-legacy
ImageJ+ImageJ2 compatibility layer

Java · 17 stars
imagej-matlab
MATLAB integration with ImageJ data structures and runtime.

Java · 16 stars
imagej-updater
The automatic updater for ImageJ

Java · 13 stars
imagej-omero
Server- and client-side communication between ImageJ and OMERO

Java · 12 stars
imagej-ui-swing
ImageJ UI for Java Swing.

Java · 12 stars
imagej-common
ImageJ core data model

Java · 12 stars
imagej-itk
ITK integration for ImageJ

Java · 8 stars
16 more repositories live on View on GitHub

Beginner friendly Everything

Open All

JPype optimization notice Open

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

imagej/pyimagej#342 · 1 reaction · Opened Aug 14, 2026
False positive `Conflicts` for same `artifactId` Open

Difficulty 3/5 1-2 days Newbie friendliness 68/100

imagej/imagej-updater#120 · 3 comments · Opened Jun 26, 2026
Overlays don't show for compressed multi-page tifs Open

Difficulty 4/5 3-5 days Newbie friendliness 68/100

imagej/ImageJ#296 · Opened Jun 9, 2026
Make "Hello world" the default template for new scripts Open

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

imagej/imagej-scripting#40 · Opened Jun 5, 2026
Promote some templates into script plugins Open

imagej/imagej-scripting#39 · 5 comments · 1 assignee · Opened Jun 5, 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
ImageJ bug only under mango Open

Difficulty 4/5 3-5 days Newbie friendliness 45/100

imagej/ImageJ#293 · Opened Apr 16, 2026
Update site URLs should trim whitespace Open

enhancement

Difficulty 2/5 1-3 hours Newbie friendliness 62/100

imagej/imagej-ui-swing#96 · Opened Feb 11, 2026
Consider a live script example showing a simple MATLAB use case of ImageJ-MATLAB Open

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

imagej/imagej-matlab#31 · Opened Feb 9, 2026
Assess & update the impact of the Javascript transition on ImageJ-MATLAB installation Open

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

imagej/imagej-matlab#30 · Opened Feb 9, 2026
Suggestion: link this ImageJ-MATLAB repository to File Exchange Open

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

imagej/imagej-matlab#29 · Opened Feb 9, 2026
Make "Scale" command optionally multi-threaded Open

Difficulty 4/5 3-5 days Newbie friendliness 45/100

imagej/ImageJ#290 · Opened Dec 15, 2025
The threadpool executer in ThreadUtil prevents the JVM from exiting. Open

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

imagej/ImageJ#287 · 4 comments · 2 reactions · Opened Dec 11, 2025
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
Particle analysis - strange behaviour Open

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

imagej/ImageJ#286 · 6 comments · Opened Nov 6, 2025
Some problems with ScaleBar (second issue) Open

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

imagej/ImageJ#284 · Opened Sep 28, 2025
Some problems with ScaleBar (first issue) Open

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

imagej/ImageJ#283 · Opened Sep 28, 2025
Support Python 3.13 Open

imagej/napari-imagej#332 · 1 assignee · Opened Sep 23, 2025
Updated ContrastAdjuster.java Open

Difficulty 4/5 3-5 days Newbie friendliness 43/100

imagej/ImageJ#281 · 4 comments · 1 reaction · Opened Aug 23, 2025
Napari-imagej mamba installation is out of date Open

Difficulty 1/5 Under an hour Newbie friendliness 78/100

imagej/napari-imagej#330 · 1 reaction · Opened Aug 12, 2025
Documentation is wrong about installing from source Open

Difficulty 1/5 Under an hour Newbie friendliness 30/100

imagej/napari-imagej#329 · Opened Aug 12, 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
Citation info should be on the RTD page, not just the README Open

documentation

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

imagej/napari-imagej#327 · 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
PROTECTED_LOCATION logic does not fully work Open

bug

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

imagej/imagej-updater#118 · Opened Jul 18, 2025
Scheduled removal of Applets from Java Open

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

imagej/ImageJ#278 · 1 comment · Opened Jul 17, 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
[Fiji] Plugin issues: Source file not up-to-date: Adjustable_Watershed.java, Measure_Roi_PA.java. ClassNotFound. Open

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

imagej/ImageJ#275 · Opened Jun 23, 2025
SCIFIO doesn't work when opening files in an ImageJ macro Open

bug

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

imagej/imagej-legacy#317 · Opened Mar 17, 2025
Invalid open command when using macro recorder Open

bug

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

imagej/imagej-legacy#316 · 3 comments · Opened Mar 17, 2025
Problem opening and saving image sequences on Mac OS Open

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

imagej/ImageJ#272 · Opened Mar 9, 2025
imagej2/fiji Could not initialize class javax.imageio.ImageIO Open

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

imagej/imagej2#318 · Opened Feb 28, 2025
Index error when performing Equalization of stacked histogram Open

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

imagej/ImageJ#271 · 1 comment · Opened Feb 27, 2025
In ROI manager, stroke color and fill color cannot be set at the same time Open

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

imagej/ImageJ#269 · Opened Feb 19, 2025
Help message improvements. Open

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

imagej/ij1-patcher#55 · Opened Feb 12, 2025
Certain RankFilters() operations never report system exit, hang indefinitely Open

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

imagej/imagej2#317 · 1 comment · Opened Feb 4, 2025
Problematic modification in opening ome.tiff files Open

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

imagej/ImageJ#268 · 3 comments · Opened Feb 3, 2025
DefaultDatasetView out of bounds error Open

Difficulty 3/5 1-2 days Newbie friendliness 55/100

imagej/imagej-common#113 · Opened Jan 17, 2025
Tests fail on WSL2 Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 30/100

imagej/imagej-updater#114 · 2 comments · Opened Jan 9, 2025
Unresponsive menu "install plugin" Open

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

imagej/ImageJ#264 · 1 comment · Opened Dec 20, 2024
8-bit ND2 files stretch bug Open

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

imagej/ImageJ#263 · 3 comments · Opened Dec 16, 2024
Array.fourier() first value incorrectly calculated Open

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

imagej/ImageJ#262 · Opened Nov 28, 2024
Edits to ColorTables of ImagePlus created from a Dataset never make it back to that Dataset Open

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

imagej/imagej-legacy#311 · 4 comments · Opened Nov 18, 2024
SciJava Table outputs create new rows on error Open

bug

imagej/napari-imagej#310 · 1 assignee · Opened Nov 12, 2024
Test local installations Open

bug

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

imagej/napari-imagej#308 · 1 comment · Opened Nov 8, 2024
Enable xarray v2024.10.0+ Open

bug

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

imagej/napari-imagej#304 · 7 comments · Opened Oct 29, 2024
Add ij.run_script signature that takes file paths Open

enhancement

imagej/pyimagej#318 · 1 reaction · 1 assignee · Opened Oct 29, 2024
Build widgets for optional Module parameters Open

enhancement

imagej/napari-imagej#300 · 1 assignee · Opened Oct 15, 2024

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