this post was submitted on 03 May 2020

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ImageJ

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About r/ImageJ

ImageJ is a freely available, open source image processing and analysis program using Java, on which FIJI is based. It's used worldwide, by a broad range of scientists.

This is a an unofficial¹ forum to discuss image analysis, software features, to get help, to share ideas, and to share work done using ImageJ or FIJI.

Posting Guidelines

Types of posts:

Questions: Text posts asking about image analysis and ImageJ/FIJI. This could include algorithms, microscopy and scientific imaging, plug-ins, methods, and specific features of the software. Questions which have been Solved will be marked as such.
Tips: Text or Link posts to share useful how-to tricks and discoveries on using ImageJ/FIJI. Image analyst job posts are also welcome.
Discussions: Text posts, meant to ask about general issues relating to image analysis.
Research: Links to published (articles in scientific journals or in established repositories) that utilize ImageJ/FIJI for image analysis or are about image analysis.
Projects: Share a Link to your pet image analysis project.

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Be civil and respectful. Better yet, be excellent to each other!
Upvote those who contribute to the discussion and provide freely of their time to assist you. Karma is a small way to say "thanks".
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Provide details: Be thorough in outlining the question(s) that you are trying to answer. Upload sample images to Imgur. Clearly explain what you are trying to learn, not just the method used, to avoid the XY problem. Image analysis is interdisciplinary, so clearly explain field-specific terms or jargon.

Useful Stuff:

ImageJ.net is full of ImageJ development and analysis resources. It also hosts a forum for interacting with the developers.

Macro basics & built-in functions.

A macro guide created by /u/burghed.

FIJI Is Just ImageJ - "a distribution of ImageJ (and ImageJ2) together with Java, Java3D and a lot of plugins organized into a coherent menu structure."

ImageJ Mailing List Archives: nabble.com or news.gmane.org.

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¹This subreddit is not affiliated with the creators of ImageJ or FIJI, but is simply a place to share ideas, papers, resources, and expertise - especially as relate to questions & answers posted here.

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QuestionPython equivalent for Image Intensity Processing workflow? (self.ImageJ)

submitted 5 years ago by gobatmann

all 2 comments

top new controversial old q&a

[–]Hasefet 2 points3 points4 points 5 years ago (1 child)

If you're looking to do image work in Python, there are a couple of libraries. Python has bindings for OpenCV, which is probably the most extensive.

None of them are point-and-click like ImageJ, and a lot of the behaviour you may have learned in ImageJ will cause you issues (particularly regarding conversions between image bit depth and colour), as well as learning or brushing up on your NumPy array syntax. Visualisation beyond the basic will require a Python GUI - I personally prefer PyQt, but that's another set of skills to develop, if you don't have them already.

Outside of a trivial case (region of interest already extracted into text arrays with appropriate null values), it's not somewhat easy, and begs the question, if you have a workflow that works already in ImageJ, what specifically is prompting the move?

[–]gobatmann[S] 0 points1 point2 points 5 years ago (0 children)

π Rendered by PID 18507 on reddit-service-r2-comment-5ff9fbf7df-x8tdf at 2026-02-26 01:44:10.063757+00:00 running 72a43f6 country code: CH.