tomMEM
commented
1 year ago Solved: Update: After reinstallation of intake_io, am_utils, pylkb using phyton setup.py build for each and installation of different pytorch package (pip install torch==1.9.1+cu111 torchvision==0.10.1+cu111 torchaudio==0.9.1 etc.), things are improving. Pytest or phyton setup.py test still display some errors in the conversation script, otherwise it is fine.
run_puncta_analysis.ipynb: is running and is giving outputs image_conversation: so far no success, no error message but also no new files. setup_image_conversation: some sparse.py errors - is linked to windows path strings - .solved
Hello, I am trying your scripts to analyze puncta in fluorescence images. The sample notebooks allow to display and modify the parameter files, but I could not get any results in the output directories. I thought there might a list of ROI coordinates of detected puncta at the end, but so far, I could not get such outputs. It is copying the parameter.json and the sample tiffs into the output folder, but no further information. I installed the repository on a windows/cuda11.2 computer a few times, however without progress. It would be great to get some suggestions how to deal with this output problem. Thomas