Athul R Vijayan comments

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                                            Athul R Vijayan

3D export the "Cellprob" channel

Thanks a lot. Can one open the .npy file in image J or so and convert to tiff file? It would be really great if this can be saved as...

Erronous segmentation of the whole stack, But a cropped region works perfectly.

Hi @kevinjohncutler I have just used the cellpose GUI for performing the segmentation, not the codes. I am not sure what the Scale disk On and Off does? I already...

Erronous segmentation of the whole stack, But a cropped region works perfectly.

Hi @kevinjohncutler I rerun this with the command line cellpose- "python -m cellpose --dir ~/Cellpose_test/ --pretrained_model nuclei --diameter 15. --save_tif --use_gpu --do_3D" I have also run the same with diameter...

Erronous segmentation of the whole stack, But a cropped region works perfectly.

@kevinjohncutler. Thanks a lot for the update. Just that it's clear for me. How/Where do I change the "normalize99" parameter? Is it possible when using gui? Best, Athul

Erronous segmentation of the whole stack, But a cropped region works perfectly.

Thanks a lot @kevinjohncutler, That worked for me. Best, Athul

3D export the "Cellprob" channel

Thanks a lot.