[BUG] No controls for Z slice position in latest GUI

[msymeonides]

When I load a TIFF image that has multiple Z slices into Cellpose 3.0.5 (whether by drag-and-drop or by file-load) there is no box to adjust Z slice anywhere in the GUI. Opening the same image in Cellpose 2.3.2 has the Z slice box and adjusting it works, so the image is fine.

[carsen-stringer]

please run python -m cellpose --Zstack

[msymeonides]

Thanks - sorry I tried searching issues for this but it was unsuccessful... did not know Zstack defaults to False now but I expect it will return to True once denoising works in 3D?

[msymeonides]

Hmm it reverts Z to 0 no matter what I type in when I hit Enter. When the file loads the console says:

GUI_INFO: loading image: F:/Arivis4/BKChen lab/Converted/20220614 72hr HRC/Cellpose (Feb 24)/TileScan 3_Position 15_RAW.ome.tiff - C=7.tif
2024-03-04 12:41:33,234 [INFO] reading tiff with 13 planes
100%|█████████████████████████████████████████████████████████████████████████████████| 13/13 [00:00<00:00, 277.40it/s]
WARNING: image has more than 3 channels, keeping only first 3

That's not right, the image is 1 channel with 13 planes. Loads fine in Cellpose 2.3.2.

[msymeonides]

OK, it works as expected when I drag-and-drop to open the image, if I use file-load to open the image it does what I described above.

[carsen-stringer]

ah good catch, fixing the load from File now. From now on, the 3D and 2D GUIs are separated, so please use the python -m cellpose --Zstack for 3D data

[carsen-stringer]

please pip install git+https://github.com/MouseLand/cellpose

[msymeonides]

Great, works properly now! TYSM