Save multichannel images as cyx, not zyx

[ndamond]

When multichannel images are loaded into CellProfiler and saved as tiff files using the SaveImages module the channels become slices (zyx instead of cyx), which causes problems with downstream processing.

Steps to reproduce
Example images (original image and image saved by CellProfiler): Images.zip

1. Load OriginalImage.tiff into CP (image type = Color image, intensity range = Image bit-depth, process as 3D = No)
2. Save it as tiff 16-bit using the SaveImages module
3. In the saved image channels have become slices (zyx instead of cyx).

Expected behavior
Channels should remain channels when saving multichannel images.

Desktop:

• Windows 10
• CellProfiler 3.1.9 (installed with .exe from website)

[bethac07]

Hi,

This is actually not a CellProfiler behavior, but a skimage behavior- skimage doesn't support saving >4 channels. https://github.com/CellProfiler/CellProfiler/blob/master/cellprofiler/modules/saveimages.py#L693-L696

52 channels is definitely unusual- can I ask what the overall workflow is that you're trying to preserve, and what is downstream of this so that we can brainstorm alternate routes to the same endpoint?

[ndamond]

Thanks for your answer, I found a workaround but it's not the first time I stumble on this issue.

What I was trying to do is create a new channel that is the average intensity projection of all the other channels in the stack and to add this new channel as the first slice of the stack. This with two custom CP plugins (from https://github.com/BodenmillerGroup/ImcPluginsCP, also attached in the example data below). It works with the original image but when this image is first saved via SaveImages as described above, I end up with a 4-channel color image instead of a 53 channel stack.

ExampleData.zip, contains:

• the original image (OriginalImage.tiff) and the same image saved via SaveImages (SavedImage.tiff).
• an example pipeline with the two required custom plugins.
• the output images from this pipeline (OriginalImage_output.tiff and SavedImage_output.tiff).