awedwards/bidc

MIBI pipeline from post-collection to expression data

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awedwards commented

Create a pipeline for MIBI:

  1. Fresh images loaded into IONpath
  2. Mass correction and filtering
  3. Pull from ionpath
  4. Segmentation
  5. Expression extraction

Resources for designing pipeline:
https://data.humancellatlas.org/pipelines/pipeline-best-practices#why-do-we-care-about-automation