pull functions from pipeline utils into each ophys_etl capsule

[arielleleon]

Notes 8/30:

• pipeline utils functions moved into each capsule (i.e. dont need special codebase to translate data between capsules)
• capsules are being added to github for each processing step (ex: aind-suite2p-motion-correction, aind-ophys-segmentation)

Notes on overall capsule / repo architecture:

• open question - do we want one repo / capsule for each step, or does each algorithm need its own repo / capsule? probably want one capsule per method (i.e. one capsule for suite2p segmentation, one for extract, etc)
• currently testing motion correction & segmentation capsules
• suggestion to look at Jerome's deep interpolation repo which has multiple sub-capsules that nextflow calls (this keeps the "pipeline" within a single location in GitHub rather than being "locked in" to code ocean pipeline workflow infrastructure)
• this structure allowed Matt to download the full nextflow repo and modify it a bit such that he could deploy it on the HPC
• there are also Github modules (folders within a repo that are linked to another repo)
• these are design decisions to be discussed with David

screenshot of Jerome's repo:

[arielleleon]

• [x] suite2p motion correction
• [x] segmentation
• [x] trace extraction
• [x] demixing
• [x] neuropil correction
• [x] dff

this will allow for capsule and pipeline mobility and writes relevant metadata to using the Processing project from aind-data-schema

[arielleleon]

9/6:

All capsules have been added to github, added to code ocean and have been tested. Users of this group working on algo development have been added as owners of each capsule.

Segmentation: https://codeocean.allenneuraldynamics.org/capsule/9037663/tree Trace Extraction: https://codeocean.allenneuraldynamics.org/capsule/8322700/tree Demixing: https://codeocean.allenneuraldynamics.org/capsule/4967276/tree Neuropil: https://codeocean.allenneuraldynamics.org/capsule/7531658/tree dF/F: https://codeocean.allenneuraldynamics.org/capsule/6715890/tree