Skip steps within Stitching

[FangmingXie]

New feature

I was trying to stitch a large sample. The whole stitching pipeline seems to have a few consecutive steps, including:

• parse czi tile
• czi2n5
• retile z
• flatfield correction
• stitch
• fuse

where each step could take long to complete. If the pipeline was stopped in the middle, we have to rerun the entire thing from the very beginning.

I was wondering if we can skip those steps if they have been done, in much of the same way as we can already choose to skip registration, spot_extraction, etc? Thanks!

Proposal

For example, can we skip czi2n5 if that step has been completed in a previous run? Can we choose to do fuse only, if all previous steps have been completed?

Usage scenario

This will make stitching large sample much easier than now, especially when it is run on a modest server or on a computer cluster that restricts user time.

[krokicki]

You can use the --skip parameter to skip any set of steps, as long as the files that subsequent steps expect are in the correct location.

[FangmingXie]

Thanks that I know and I am using that feature a lot -- it is very useful! However, I guess my question is: can we skip a "half" step within the stitching step? I know we can skip these steps such as: stitching, registration, spot_extraction, segmentation, warp_spots... But I am not sure if I can skip a half step within stitching if the intermediate files were there.

[krokicki]

Ah, I understand what you mean now. I think it should be possible to add this feature.

[FangmingXie]

I guess this feature is not on the top of my wish list now. So no worries.