Should ROIs and masks be removed after the image processing has finished?

[stulacy]

In the Image Processing tab, the full CellPhe pipeline is run, including the segmenting and tracking of cells. The ultimate output of this are the 2 CellPhe feature tables, both the frame level and summary level ones. However, intermediate data is also created and saved to disk, including:

• ROI files
• CellPose masks
• Trackmate CSV

None of these need to be kept permanently on disk, but in some cases it might be useful for the user to access them. There are several options:

• Make all ephemeral, i.e. delete all 3 after the image folder has been processed
• Offer the choice to the user for each one (I would default to keeping ROI files and Trackmate CSV, but not CellPose masks)

If we do allow any to be retained then it would be useful to allow the user to choose where to save them to, as the default location (in the same folder as the raw images) might not be the most appropriate for each use case.

@llwiggins Any thoughts welcome

[llwiggins]

Hi Stuart,

For our own analysis, the ROI files would be the most important to save to disk out of these 3, but perhaps this isn't the case for other users. I think we should offer the choice to the user, and perhaps default to storing just the ROIs? Would it be possible to save them to disk in a zip folder rather than unzipped?

I think it could be good to store all outputs in the same main directory as the image folder, e.g. if images are in my_experiment/images, then save everything else within my_experiment so that users have a directory containing all their outputs. What do you think?

[stulacy]

Great, thanks. I'll add in the ability to decide whether to save those 3 intermediate outputs or not, with only ROI defaulting to true (and yes I'll save them as a zip). For now I'll leave them to be saved alongside the images, although I'll document this in app.