imagej / imagej/ImageJ

Problem opening and saving image sequences on Mac OS

Open
#272 0 comments 0 reactions 0 assignees View on GitHub

Nobody has claimed this yet.

Dominant language
Java
Stars
786
Forks
267
PR merge metrics
No merged PRs in 30d

Description

In the latest ImageJ/Fiji installations on Mac OS Mojave or Sequoia I am having problems with opening and saving image sequences created with from Micromanager. The images are saved as a series of tiff files (time lapse imaging). In one example, using File/Open/Image Sequence, for a series of 300 images will open a window which says there are 2750 images and all come up as white (all pixels 255). If I use File/Open/Bioformats, the sequence will open correctly. If I now change the properties of the stack (Image/Properties, for instance from 60 seconds to 1 min, and save, it will reopen with the time set back to seconds (so it will be 1 second interval instead of 1 min) every time it is saved. The units of the pixels will also change upon save.

Contributor guide

No contributing guide indexed for this repository

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by reproducing the report on Mac OS using File/Open/Image Sequence with the described TIFF series, then compare it with File/Open/Bioformats. Check Image/Properties and the save-and-reopen behavior, including image count, pixel values, time units, and pixel units. Done means the sequence opens with correct metadata and retains those properties after saving.

Written by the indexing model from the issue text.

Assessment

Tech stack
java, macos
Domain
computer-vision
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
35/100

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.