Error while running anatomical mode in Suite2p v10.3

[NidhiGujar]

Hello! I have been trying to run Suite2p v10.3 with the anatomical mode on. However I end up getting the following error for every run-

----------- ROI DETECTION Binning movie in chunks of length 08 Binned movie [1488,170,220] in 4.52 sec. Binned movie denoised (for cell detection only) in 17.75 sec. CELLPOSE finding masks in max_proj / mean_img !NOTE! ops['diameter'] set to 5.00 for cell detection with cellpose ERROR<<< cellprob_threshold and dist_threshold are being deprecated in a future release, use mask_threshold instead 100 masks detected, median diameter = 7.86 Detected 100 ROIs, 34.53 sec ----------- Total 57.49 sec. ----------- EXTRACTION Masks created, 0.20 sec. Extracted fluorescence from 100 ROIs in 12060 frames, 9.15 sec. ----------- Total 9.82 sec. ----------- CLASSIFICATION ['skew', 'compact', 'npix_norm'] ----------- Total 0.08 sec. ----------- SPIKE DECONVOLUTION ----------- Total 0.13 sec. Plane 0 processed in 68.06 sec (can open in GUI). total = 68.27 sec. TOTAL RUNTIME 68.27 sec Interrupted by error (not finished)

Could you let me know what the issue might be and how could it be solved?

Thanks and Regards, Nidhi

[gosipe]

I am also having the same issue. I tried installing a previous version of cellpose (0.6.5) but I was getting certificate errors. Any help on this is much appreciated!

Thanks, -Gray

----------- ROI DETECTION Binning movie in chunks of length 08 Binned movie [868,492,492] in 6.35 sec. Binned movie denoised (for cell detection only) in 32.35 sec. CELLPOSE finding masks in mean_img !NOTE! ops['diameter'] set to 20.00 for cell detection with cellpose ERROR<<< cellprob_threshold and dist_threshold are being deprecated in a future release, use mask_threshold instead 86 masks detected, median diameter = 22.83 Detected 86 ROIs, 20.08 sec ----------- Total 59.87 sec. ----------- EXTRACTION Masks created, 1.56 sec. Extracted fluorescence from 86 ROIs in 7272 frames, 8.36 sec. ----------- Total 9.98 sec. ----------- CLASSIFICATION ['npix_norm', 'skew', 'compact'] ----------- Total 0.02 sec. ----------- SPIKE DECONVOLUTION ----------- Total 0.03 sec. Plane 0 processed in 70.06 sec (can open in GUI). total = 92.62 sec. TOTAL RUNTIME 92.62 sec Interrupted by error (not finished)

[christian-potter]

My lab has an identical bug on several computers (with suite2p v 10.3), and the issue persists when we upgraded those computers from cellpose v 1.0 to 2.0

[carsen-stringer]

consolidating issues: #794

[carsen-stringer]

this should be fixed now