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BactoScoop documentation
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BactoScoop documentation

Getting started

  • Installation
  • CPU and GPU segmentation
  • Quick start
  • Images, channels, and masks
  • Outputs

Analysis workflow

  • Segmentation and mask review
  • Contours, midlines, and meshes
  • SVM curation
  • Channel alignment and shift correction
  • Intracellular object detection
  • Feature extraction
  • Signal correlation and similarity
  • Merge tables and save results
  • Processing summaries and logging

Examples

  • Three-channel walkthrough: DAPI and GFP-DnaN objects
  • Five-channel walkthrough: membranes and multichannel profiles
  • Reuse masks and saved meshes
  • Plotting and visual quality control
  • Parallel processing of sample folders

Reference

  • Feature dictionary
    • Morphological features
    • Profiling features
    • Objects features
    • Membrane features
    • Svm features
  • Parameter reference
  • API reference
    • bactoscoop.curation
    • bactoscoop.features
    • bactoscoop.image
    • bactoscoop.imagecollection
    • bactoscoop.logging_utils
    • bactoscoop.omni
    • bactoscoop.plot
    • bactoscoop.signalcorrelation
    • bactoscoop.utilities
  • Data structures and coordinate conventions
  • Troubleshooting
  • Project information
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