imagej / imagej/imagej-matlab

Handling of a multi-dimensional image by IJM.show()

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#17 2 comments 0 reactions 0 assignees View on GitHub
Dominant language
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/10156/7), I'd like to raise an issue `aboutIJM.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 this method does not really support multi-dimensional or multi-channel images well. Whatever the dimensions are, all the channels are always treated as a stack of single-channel images.

It would be much nicer if one specifies a rule about which dimension of input MATLAB array represent what (X, Y, Z, channel, time etc) and `IJM.show()` handle it internally to prepare an appropriate object in ImageJ.

This issue is also related, but more specifically about X and Y axes.

https://github.com/imagej/imagej-matlab/issues/16

Contributor guide

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Research direction

Start with IJM.show() and net.imagej.matlab.ImageJMATLABCommands.show(), then review the linked issue and forum discussion for existing axis conventions. Define how MATLAB dimensions map to X, Y, Z, channel, and time, and verify that multi-dimensional and multi-channel inputs become appropriate ImageJ objects rather than single-channel stacks.

Written by the indexing model from the issue text.

Assessment

Tech stack
java, matlab
Domain
data, desktop
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
30/100

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