for question relate the Stardist(2D and 3D) 5.2 error mapping and quality metrics estimation

[jinxsfe]

Describe the bug

As for 5.2 error mapping and quality metrics estimation, for annotation # modify the names to suitable form: path_images/_numberX.tif

I can't run successfully due to setp error below for the step " imsave(names[i],labels ,polygons)"

but when I delete polygons, and imsave(names[i],labels )" like this, the picture will generate , I don't know why I can save without polygons and what effect if I delete thems?

Expected behavior A clear and concise description of what you expected to happen.

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macbookpro

[guijacquemet]

Hi @jinxsfe Thanks for reaching out. I am not sure I understand your issue. Could you post a screenshot of the error you get?

Thanks

Guillaume

[jinxsfe]

Hi @jinxsfe Thanks for reaching out. I am not sure I understand your issue. Could you post a screenshot of the error you get?

Thanks

Guillaume

Hello, Guija, Thanks for help!

This is Stardist 3D model, as you see, when I run the code in secton 5.2 (name:error mapping and quality matrics estimation, it show the error informations in here,

the major problem is here, imsave(names[i], labels, polygons), I can run when I delete polygons, just leave names[i] and labels, but I had remembered polygons is used to build to 3D, I don't know whether good or not to delete polygons, do you have better solutions for here? I am worried that will cause bad effect in predictions(may show the 2D instead of 3D, because stardist 2D models don't have polygons in here), Do you have any comments for that?

[jinxsfe]

I also have question for that when I put the real data(19.511,511), does some possible that I can run it without reduce the size of image? I am afraid the information will be loss, if I would reduce x y to half of 511. I try to use grid = (1,8,8) instead of 4 but faild, fov is (16,73,73) which is also small, does some possible situation to increase that problem?

[guijacquemet]

Hi, @jinxsfe I have now uploaded a new version of the StarDist 3D notebook that should fix the first issue you reported.

Best wishes

Guillaume

[guijacquemet]

Hi, I am now closing this issue. Let me know if you still have problems.