BIOP / qupath-extension-cellpose

an extension that wraps a Cellpose environment such that WSI can be analyzed using Cellpose through QuPath.
Apache License 2.0
63 stars 11 forks source link

Select save and temp folders during builder #27

Closed lacan closed 1 year ago

lacan commented 1 year ago

From a forum post: https://forum.image.sc/t/qupath-extension-cellpose-for-qupath-0-4-0/75074/40?u=oburri

Does an option exist to specify the directory where cellpose-temp and cellpose-training files are written to? If not, i think it could be a handy feature to add for remote stored projects, or large projects being analysed on multiple workstations.

For projects stored on remote servers, it is possible to move files locally for certain aspects of analysis to speed up read/write aspects of analysis QuPath project analysis speed up by using multiple workstations? - Image Analysis - Image.sc Forum. However, i notice that even if i move the image files locally, cellpose still writes cellpose-temp files to the remote server.

For large projects, where one can split .qproj into 2 parts, to run cellpose on 2 workstations, as they are both trying to write to the same ‘cellpose-temp’ folders within the qupath project, i worry both workstations would try to write files to the same directory and this would potentially cause issues.

imagesc-bot commented 1 year ago

This issue has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/qupath-extension-cellpose-for-qupath-0-4-0/75074/41

lacan commented 1 year ago

Done