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

[kouichi-c-nakamura]

Following discussion in here, 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, 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.

#17

[kouichi-c-nakamura]

IJM.show() in ImageJ-MATLAB does not support multi-dimentional or multi-channel images
http://forum.imagej.net/t/ijm-show-in-imagej-matlab-does-not-support-multi-dimentional-or-multi-channel-images/10156/7

[kouichi-c-nakamura]

I wrote a wrapper function of IJM.show called ijmshow, and it can handle the X and Y axes nicely.

https://github.com/kouichi-c-nakamura/ijmshow/

[imagejan]

This issue doesn't only affect IJM.show() but in general the conversion between IJ and Matlab. For example, data input by #@ script parameters suffer from the same issue:

• #@matrix data -> y * x
• imread(path-to-file) -> x * y