analysis_config.yaml

fish:
  PreprocessingFishFlatFieldKernel:
  - 1
  - 100
  - 100
  PreprocessingFishFilteringSmallKernel:
  - 1
  - 8
  - 8
  PreprocessingFishFilteringLaplacianKernel:
  - 0.02
  - 0.01
  - 0.01
  CountingFishMinObjDistance: 1
  CountingFishMaxObjSize: 200
  CountingFishMinObjSize: 1
  CountingFishNumPeaksPerLabel: 20
  LargeObjRemovalPercentile: 95
  LargeObjRemovalMinObjSize: 100
  LargeObjRemovalSelem: 3
both-beads:
  PreprocessingFishFilteringSmallKernel:
  - 1
  - 8
  - 8
  PreprocessingFishFilteringLaplacianKernel:
  - 0.02
  - 0.01
  - 0.01
  PreprocessingFishFlatFieldKernel:
  - 1
  - 100
  - 100
  CountingFishMinObjDistance: 5
  CountingFishMaxObjSize: 600
  CountingFishMinObjSize: 10
  CountingFishNumPeaksPerLabel: 1
  LargeObjRemovalPercentile: 95
  LargeObjRemovalMinObjSize: 100
  LargeObjRemovalSelem: 3
staining:
  PreprocessingStainingFlatFieldKernel:
  - 2
  - 100
  - 100
fresh-tissue:
  nuclei:
    PreprocessingFreshNucleiLargeKernelSize:
    - 5
    - 50
    - 50
  beads:
    PreprocessingFishFlatFieldKernel:
    - 100
    - 100
    CountingFishMinObjDistance: 20
    CountingFishMaxObjSize: 200
    CountingFishMinObjSize: 20
    CountingFishNumPeaksPerLabel: 1
BarcodesExtractionResolution: 2
RegistrationReferenceHybridization: 1
RegistrationTollerancePxl: 3
RegistrationMinMatchingBeads: 5