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HenriquesLab / ZeroCostDL4Mic

ZeroCostDL4Mic: A Google Colab based no-cost toolbox to explore Deep-Learning in Microscopy
MIT License
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Cellpose issue: imwrite() got an unexpected keyword argument 'compress' #230

Closed jbogomolovas2 closed 1 year ago

jbogomolovas2 commented 1 year ago

When I do batch processing of images in section 6.1 I get the following error: TypeError: imwrite() got an unexpected keyword argument 'compress' Is there any way of fixing it?

Screenshot 2022-12-15 at 2 35 18 PM
Marien-kaefer commented 1 year ago

Hi ZerCost Team,

I and other users of our facility are facing the same issue as the person above. Using a built-in model, the preview is generated and looks as I would hope/expect but the images cannot be written onto the G drive. In addition, there is an error message in the first code cell - just in case these two problems are related: |████████████████████████████████| 69 kB 3.9 MB/s Building wheel for folium (setup.py) ... done ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts. datascience 0.17.5 requires folium>=0.9.1, but you have folium 0.2.1 which is incompatible. Is this anything you could help with?

jbogomolovas2 commented 1 year ago

I found a way to fix imwrite() error by forcing to install older version of tifffile, in section 1: !pip install -q tifffile==2022.4.8