INFO: Cellpose2D: 10:28:29,854 not all flows are present, running flow generation for all images INFO: Cellpose2D: 10:28:29,852 TORCH CUDA version not installed/working. INFO: Cellpose2D: 10:28:29,850 WRITING LOG OUTPUT TO /Users/christianblok/.cellpose/run.log INFO: This command should run directly if copy-pasted into your shell INFO: Found 3 Training objects and 3 Validation objects in image 2.2_73_MouseSNDAPI_TH488_2Me594.vsi - 20x_FITC, C圓, DAPI_01Ģ.2_73_MouseSNDAPI_TH488_2Me594.vsi - 20x_FITC, C圓, DAPI_01_region_0.tifĢ.2_73_MouseSNDAPI_TH488_2Me594.vsi - 20x_FITC, C圓, DAPI_01_region_0_masks.tifĢ.2_73_MouseSNDAPI_TH488_2Me594.vsi - 20x_FITC, C圓, DAPI_01_region_1.tifĢ.2_73_MouseSNDAPI_TH488_2Me594.vsi - 20x_FITC, C圓, DAPI_01_region_1_masks.tifĢ.2_73_MouseSNDAPI_TH488_2Me594.vsi - 20x_FITC, C圓, DAPI_01_region_2.tifĢ.2_73_MouseSNDAPI_TH488_2Me594.vsi - 20x_FITC, C圓, DAPI_01_region_2_masks.tifīash -c "/Library/anaconda3/envs/cellpose/bin/python -W ignore -m cellpose -train -dir "/Users/christianblok/QuPath/v0.4/Cellpose training/Training and validation/cellpose-training/train" -test_dir "/Users/christianblok/QuPath/v0.4/Cellpose training/Training and validation/cellpose-training/test" -pretrained_model cyto -use_gpu -verbose" INFO: If tiling is necessary, 60 pixels overlap will be taken between tiles Use `.setOverlap( int )` to modify overlap INFO: Neither diameter nor overlap provided. I have used the training script provided by Olivier Burri.Made training and validation ROI’s and delineated cells within these ROI’s. Installed cellpose in Qupath + setting the path to python in the extensions preferences.Downloaded anaconda and installed cellpose (I can open it from my terminal).I have trouble with Cellpose in qupath, things I already did:
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