imagej / imagej/imagej-matlab

Handling of X and Y axes of an image by IJM.show()

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Java
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Description

Following discussion in [here](http://forum.imagej.net/t/ijm-show-in-imagej-matlab-does-not-support-multi-dimentional-or-multi-channel-images/10156/3), I'd like to raise an issue about` IJM.show()`.

`IJM.show('I')` or `net.imagej.matlab.ImageJMATLABCommands.show('I')` is a great way to transfer array data from MATLAB workspace to ImageJ, thanks to `ImageJ-MATLAB`.

However, I’ve noticed that X and Y of axes of images are flipped over between MATLAB and ImageJ, which is not smart at all.

MATLAB's `permute` can manipulate data to avoid this problem. But, because it apparently needs to [copy data internally](https://stackoverflow.com/questions/36065182/why-does-matlabs-permute-not-need-extra-memory), it requires double memory, which is not ideal. An imglib2 /ImageJ2 -style permute (which re-indexes but does not copy) might be a better solution.

This issue is also related, but more specifically about multidimensional images.

https://github.com/imagej/imagej-matlab/issues/17

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  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 at the IJM.show('I') and net.imagej.matlab.ImageJMATLABCommands.show('I') entry points, then compare MATLAB and ImageJ X/Y axis conventions. Review the related multidimensional-image issue #17 and verify that transferred images retain the expected orientation without requiring MATLAB permute.

Written by the indexing model from the issue text.

Assessment

Tech stack
java, matlab
Domain
api
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
38/100

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