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KnottLab / codex

Pipeline processing CODEX output
MIT License
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Leica outputs in a secondary directory structure #21

Closed nathanin closed 3 years ago

nathanin commented 3 years ago

For some unknown reason we've encountered a directory structure like this:

[base_path]/[sample_id]/
  [timestamp]--[sample_id]/
    Metadata/
    Region 1/
    Region 2/
    TileScan 1/
      Metadata/
        Region 1.xlif
        Region 2.xlif
      Region 1--Stage00--Z00--C00.tif
      Region 1--Stage00--Z00--C01.tif
      ...

A command line switch & subsequent parsing logic is needed to read raw data in this format.

nathanin commented 3 years ago

3161e1b