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  • Installation
  • API Documentation
  • Examples
    • Introducing the Girder API
    • Procedure for managing a typical annotation project
    • Tips for scaling annotation rendering
    • Local backup and SQL querying of annotation data
    • Creating gallery images for annotation review
    • Local processing of whole-slide images using large_image
    • Color Deconvolution
    • Color normalization
    • “Smart” color augmentation
    • Nuclei Segmentation
    • Positive pixel count and parallel processing with Dask
    • Converting annotations to semantic segmentation mask images
    • Converting annotations to object segmentation mask images
    • Converting masks back to annotations
    • Merging annotations from tiled arrays
    • Merging polygons (general purpose)
    • Tissue Detection
    • Color thresholding semantic segmentation
    • Finding cellular regions with superpixel analysis
    • Analyzing remotely hosted images with the girder client
  • Contributing
  • Credits
HistomicsTK
  • Examples
  • View page source

Examples¶

  • Introducing the Girder API
  • Procedure for managing a typical annotation project
  • Tips for scaling annotation rendering
  • Local backup and SQL querying of annotation data
  • Creating gallery images for annotation review
  • Local processing of whole-slide images using large_image
  • Color Deconvolution
  • Color normalization
  • “Smart” color augmentation
  • Nuclei Segmentation
  • Positive pixel count and parallel processing with Dask
  • Converting annotations to semantic segmentation mask images
  • Converting annotations to object segmentation mask images
  • Converting masks back to annotations
  • Merging annotations from tiled arrays
  • Merging polygons (general purpose)
  • Tissue Detection
  • Color thresholding semantic segmentation
  • Finding cellular regions with superpixel analysis
  • Analyzing remotely hosted images with the girder client
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