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SchmollerLab / Cell_ACDC

A Python GUI-based framework for segmentation, tracking and cell cycle annotations of microscopy data
BSD 3-Clause "New" or "Revised" License
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Add multi-channel functionality to Cellpose in Cell-ACDC #178

Open ElpadoCan opened 1 year ago

ElpadoCan commented 1 year ago

As pointed out in #177 , cellpose in ACDC doesn't support the second channel.

dfgdgdfgd commented 1 year ago

Hi Francesco, i think, this issue can also be closed? It works now pretty good, but i found a tiny error ;) If i try to segment only nuclei, then in general i would not choose a second channel. But doing so, i get the following error message, since it seem to search for a 2. channel:

Importing cellpose...

nuclei << model set to be used

model diam_mean = 17.000 (ROIs rescaled to this size during training)

Loading Position_1\Images\YAP_1-150-3_s1_Nuklei.tif...

Segmentation file YAP_1-150-3_s1_segm_nuclei.npz... Traceback (most recent call last): File "D:\Programme\Anaconda3\envs\acdc\lib\site-packages\cellacdc\segm.py", line 261, in run second_ch_data = secondChImgData UnboundLocalError: local variable 'secondChImgData' referenced before assignment

But choosing for the 2. channel also the nuclei tif, then it works....

Thanks & best Mario

ElpadoCan commented 1 year ago

Oh yes you are right, that's a bug, I will fix it now, thanks for reporting it!

github-actions[bot] commented 1 year ago

Hi, this issue had no activity for more than 180 days. For now, we have marked it as "dormant" until there is some new activity. The reason is that we haven't had the time to implement this or it requires more discussion. Note that it doesn't mean it has been ignored, but a little reminder from your side would help :D. Feel free to reach out to us here or on our forum. If you think that this issue is no longer relevant, you may close it by yourself. In any case, we apologise for the inconvenience and we thank you for your patience and contributions so far!