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Ecosystem

  • Installation
  • Workflow
    • Package Design
    • scPortrait Projects
    • Config Files
    • SpatialData
    • Segmentation
    • Single-cell image datasets
    • Featurization Methods
  • Tutorials
    • A Walk Through The scPortrait Ecosystem
    • Different segmentation workflows
    • Fine Tuning single-cell image extraction
    • Deep learning with scPortrait
    • Automatically parse image files from Opera Phenix imaging experiments
    • Stitch individual tif files into whole-slide images

Code Examples

  • Code Snippets
  • Example Projects
    • Sharded Cellpose Segmentation
    • Sharded Cellpose Segmentation on human protein atlas images

Module API

  • pipeline
    • project
    • segmentation
    • segmentation workflows
    • extraction
    • Featurization
    • selection
  • processing
  • plotting
    • scportrait.plotting.add_scalebar
    • scportrait.plotting.colorize
    • scportrait.plotting.generate_composite
  • io
  • tools
    • parse
    • stitch
    • ml
    • h5sc
    • sdata
  • .ipynb

Example Projects

Example Projects#

Sharded Cellpose Segmentation
Sharded Cellpose Segmentation on human protein atlas images

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Run Segmentation Method on any input image

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Sharded Cellpose Segmentation

By Sophia Mädler and Niklas Schmacke

© Copyright 2026 Sophia Mädler and Niklas Schmacke.