Set pyramid `downscale_factor=2` for compatibility with recyze

labsyspharm / mcmicro

Multiple-choice microscopy pipeline

https://mcmicro.org/

MIT License

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Set pyramid `downscale_factor=2` for compatibility with recyze #490

Closed Yu-AnChen closed 1 year ago

Yu-AnChen commented 1 year ago

Palom defaults to write 4x downscale pyramid which requires changes of an unexposed parameter in recyze. This PR set the downscale factor to 2x and also allows combining multiple images into a single pyramid.

ArtemSokolov commented 1 year ago

Confirming that the following now works for exemplar-002:

workflow:
  tma: true
  viz: true
  segmentation: mesmer
  segmentation-recyze: true
  segmentation-channel: 1