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Contents:

  • 1. Quick Start
    • 1.1. Installation from Github
    • 1.2. Generating Shapes
    • 1.3. Using the py-lmd tools
    • 1.4. Numbers and Letters
    • 1.5. Text
  • 2. Using Segmented Images
    • 2.1. Background
    • 2.2. Different Coordinate Systems
    • 2.3. Getting started with the SegmentationLoader
    • 2.4. Overview of Configuration
    • 2.5. Processing Order
  • 3. Example Notebooks
    • 3.1. Generate a Cutting XML from segmentation mask using the Segmentation Loader.
      • 3.1.1. Load Segmentation Mask
      • 3.1.2. Define cell sets
      • 3.1.3. Calibration points
      • 3.1.4. XML generation
      • 3.1.5. write to XML
    • 3.2. Generate cutting XML from exported results from QUPath
      • 3.2.1. Import libraries and define helper functions
      • 3.2.2. Import GEOjson regions
      • 3.2.3. Calibration points
      • 3.2.4. Clean up Dataframe
      • 3.2.5. Generate shape collection
      • 3.2.6. write to XML
    • 3.3. Convert SVG graphic into LMD excision instructions
      • 3.3.1. Visualize Results
      • 3.3.2. Export to XML
  • 4. py-lmd Modules
    • 4.1. lmd.lib
      • 4.1.1. Collection
        • Collection
          • Collection.shapes
          • Collection.calibration_points
          • Collection.orientation_transform
          • Collection.add_shape()
          • Collection.join()
          • Collection.load()
          • Collection.new_shape()
          • Collection.plot()
          • Collection.save()
          • Collection.stats()
          • Collection.svg_to_lmd()
      • 4.1.2. Shape
        • Shape
          • Shape.from_xml()
          • Shape.to_xml()
      • 4.1.3. SegmentationLoader
        • SegmentationLoader
          • SegmentationLoader.check_cell_set_sanity()
          • SegmentationLoader.load_classes()
    • 4.2. lmd.tools
      • ellipse()
      • get_rotation_matrix()
      • glyph()
      • glyph_path()
      • makeCross()
      • rectangle()
      • text()
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© Copyright 2023 Georg Wallmann, Sophia Mädler and Niklas Schmacke.

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