MaxProjection +SaveImage Modules not working


I’ve constructed a pipeline uploading Z stacks. I got the metadata, namesandtypes and groups working.
However, the Saveimages module does not save the images

  1. All the images are not being saved
  2. nothing shows up in the output file.


Hi! AFAIK SaveImages should work with 3D images… do you mind uploading a pipeline? That’ll make it much easier to diagnose. Sufficient images to reproduce would be great too, but I guess that might be big/annoying to provide online somewhere we can access.

IF63_MaxProjection.cpproj (914.2 KB)

Thanks so much for quick reply. I’ve been trying to figure this out for hours.

Can you try setting “when to save” to first instead of last? And maybe “every” if that doesn’t work.

Also - “overwrite existing files without warning” is a pretty scary setting! Use caution!

(and if you’re still having trouble, can you clarify - is an error produced or rather everything seems to run just fine but you just don’t get the output you want?)

no error is produced.

as of now, just 1 image is saved to the folder. And the only image saved is the last one on the list.

I’ve dragged only two images into the pipeline and get a max projection of the 2nd one only.

this doesn’t work with make projection. you have to do last cycle or you get an red X next to module heading.

I mean I get a SAVED maxprojection of the 2ns one only**

Ah, ok, then I suspect it’s a problem with grouping settings (or some rare bug unique to your setup). Do you mind uploading a .cpproj with a minimal set of images that reproduce the problem (like a pair, as you mention).

Does the MakeProjection module actually produce the right image, of image 1 + 2 maxed? I see you have that window hidden (closed eyeball) so if you open that eyeball I’m curious whether MakeProjection produces the correct image and it’s just a SaveImages problem.

I uploaded such a pipeline already…

Right - but without the actual image files it’s hard to test anything. If I remember right, the .cpproj file refers to dozens of individual images, it would be best for it to have the minimal number so you don’t have to upload so many images.

(and I’m going on vacation for a week now, so hopefully someone can take over once you provide the image file and a slimmer .cpproj file!)

ah ok i thought it had two images in there…will upload in a sec

also the makeprojectino pipeline produces the correct maxprojection for both images.

IF63_MaxProjection.cpproj (898.9 KB)

thanks for your time:)

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To clarify this part: it should make a single projection for the pair of images, right? And you see this correct image during the second image cycle?

No I load about 41 image slices per image. There are 2 images. So 82 slices.

it should make a single projection for EACH set of 41 slices.

I see the correct image produced(maxprojected) for both images.

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