conda.bat path

[ZhaoJK]

Hi,

It is amazing to setup cellpost under BIOP.
However, I am working within intranet and cannot modify PATH. I would like to request conda.bat setup unde Cellpose.
create new text input for conda.batl
or modify conda.bat path by adapting from cellpose env, like CellposeEnvDir -> "D:\Anaconda3\envs\cellpose", then conda.bat -> "D:\Anaconda3\condabin\conda.bat".

Thanks a lot!

[lacan]

Hello and thanks for the message.
Perhaps a workaround would be to configure the cellpose wrapper as follows:
Environment type: Python Venv
Cellpose environment name or directory : path/to/your/conda/env/python.exe/folder

Perhaps that way you can use it. I will try and test it myself

EDIT: IT DOESN'T WORK, I will make a new release
I will think about adding that extra layer you are requesting in case this does not work

[lacan]

So I have done the following and it works as expected on the last release of the extension
See 8786d4e
And tag v0.3.7

Install Cellpose with Cuda 11.3 GPU Support

conda create - cellpose-test python=3.8
conda activate cellpose-test
pip install cellpose
pip uninstall torch
pip install torch --extra-index-url https://download.pytorch.org/whl/cu113

Find the Python Executable

where python
C:\Users\oburri\.conda\envs\cellpose-test\python.exe

Use that path in the latest version of the Cellpose Extension

And Select Python Executable under "Cellpose Environment Type"

Run Cellpose and try it

Here is my result

INFO: Starting script at Thu Jun 23 13:30:09 CEST 2022
INFO: Using Cellpose Normalization (per tile).
INFO: Using global normalization with a downsampling factor of 8
INFO: If tiling is necessary, 0 pixels overlap will be taken between tiles
INFO: Folder creation of XXXXXXXXXXXXXXXX\cellpose-temp was interrupted. Either the folder exists or there was a problem.
INFO: Saving images for 1 tiles
INFO: Saving to XXXXXXXXXXXXXXXX\cellpose-temp\Temp_10511_10362.tif
INFO: Executing command: [cmd.exe /C C:\Users\oburri\.conda\envs\cellpose-test\python.exe -W ignore -m cellpose --dir N:\public\marine.bruand_UPORICCIO\BCL6_CTSS_Mut_20220309\20220309_Update_Oli\cellpose-temp --pretrained_model cyto --chan 0 --chan2 0 --diameter 0.0 --flow_threshold 0.4 --save_tif --no_npy --use_gpu --verbose]
INFO: Cellpose2D: 2022-06-23 13:30:15,639 [INFO] WRITING LOG OUTPUT TO C:\Users\oburri\.cellpose\run.log
INFO: Cellpose2D: 2022-06-23 13:30:15,875 [INFO] ** TORCH CUDA version installed and working. **
INFO: Cellpose2D: 2022-06-23 13:30:15,876 [INFO] >>>> using GPU
INFO: Cellpose2D: 2022-06-23 13:30:15,880 [INFO] >>>> running cellpose on 1 images using chan_to_seg GRAY and chan (opt) NONE
INFO: Cellpose2D: 2022-06-23 13:30:15,880 [INFO] ** TORCH CUDA version installed and working. **
INFO: Cellpose2D: 2022-06-23 13:30:15,880 [INFO] >>>> using GPU
INFO: Cellpose2D: 2022-06-23 13:30:15,880 [INFO] >> cyto << model set to be used
INFO: Cellpose2D: 2022-06-23 13:30:17,088 [INFO] >>>> model diam_mean =  30.000 (ROIs rescaled to this size during training)
INFO: Cellpose2D: 2022-06-23 13:30:17,089 [INFO] >>>> estimating diameter for each image
INFO: Cellpose2D: 2022-06-23 13:30:17,092 [INFO] 0%|          | 0/1 [00:00<?, ?it/s]
INFO: Cellpose2D: 2022-06-23 13:30:17,106 [INFO] ~~~ ESTIMATING CELL DIAMETER(S) ~~~
INFO: Cellpose2D: 2022-06-23 13:30:19,723 [INFO] estimated cell diameter(s) in 2.62 sec
INFO: Cellpose2D: 2022-06-23 13:30:19,723 [INFO] >>> diameter(s) = 
INFO: Cellpose2D: 2022-06-23 13:30:19,723 [INFO] [ 22.92 ]
INFO: Cellpose2D: 2022-06-23 13:30:19,723 [INFO] ~~~ FINDING MASKS ~~~
INFO: Cellpose2D: 2022-06-23 13:30:20,933 [INFO] >>>> TOTAL TIME 3.83 sec
INFO: Cellpose2D: 2022-06-23 13:30:20,945 [INFO] 100%|##########| 1/1 [00:03<00:00,  3.85s/it]
INFO: Cellpose2D: 2022-06-23 13:30:20,946 [INFO] 100%|##########| 1/1 [00:03<00:00,  3.85s/it]
INFO: Cellpose2D: 2022-06-23 13:30:20,946 [INFO] >>>> completed in 5.070 sec
INFO: Virtual Environment Runner Finished
INFO: Cellpose command finished running
INFO: Getting objects for XXXXXXXXXXXXXXXX\cellpose-temp\Temp_10511_10362_cp_masks.tif
INFO: Getting objects for XXXXXXXXXXXXXXXX\cellpose-temp\Temp_10511_10362_cp_masks.tif Done
INFO: Making measurements for Annotation (Rectangle)
INFO: Done!
INFO: Script run time: 14.28 seconds