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hubmapconsortium / codex-pipeline

CODEX data processing code
GNU General Public License v3.0
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Incorporating stitching and other changes #16

Closed VasylVaskivskyi closed 3 years ago

VasylVaskivskyi commented 3 years ago
  1. Added two stitching steps. The first runs the Bigstitcher before the segmentation. Then the result is split back into tiles. The second runs after the segmentation and assembles image and mask tiles.
  2. Replaced two steps for running Cytokit with one. It doesn't require additional scripts injected into Cytokit container.
  3. Created another container for Fiji + Bigstitcher to speed up building of the container with scripts, but it can be removed in the future. This container needs to be moved to the HuBMAP docker account.
  4. In container with scripts I replaced python container base with ubuntu container base + anaconda. I did that because of problems with tifffile package.