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Methods to add #12

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12 of 37 tasks
LouisK92 opened this issue Dec 13, 2024 · 0 comments
Open
12 of 37 tasks

Methods to add #12

LouisK92 opened this issue Dec 13, 2024 · 0 comments
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enhancement New feature or request

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@LouisK92
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LouisK92 commented Dec 13, 2024 •
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segmentation

  • watershed,
  • Cellpose
  • cellpose v3+
  • Stardist,
  • Mesmer
  • binning,
  • SCS (designed for sequencing based ST, but also applicable to iST)

segmentation modification

  • nuclear expansion

transcript assignment

cell volume calculation

  • convex hull
  • nuclear segmentation
  • cell segmentation
  • alpha shape

normalization

  • normalize by total counts
  • normalize by area (ref1, ref2) --> how to set factor?
  • SpaNorm

cell type annotation

expression correction

  • sc ref based probe efficiency correction
  • nr of probes based efficiency correction
  • resolVI

qc filter

  • ...
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@LouisK92 @Kraftfahrzeughaftpflichtversicherung