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Documentation

  • 1. Quick Start
  • 2. Using Segmented Images
  • 3. Example Notebooks
    • 3.1. Generate a Cutting XML from segmentation mask using the Segmentation Loader.
    • 3.2. Generate cutting XML from exported results from QUPath
    • 3.3. Convert SVG graphic into LMD excision instructions
    • 3.4. Generate Calibration Cross Templates for PPS membrane slides
  • 4. API
    • 4.1. lib
    • 4.2. tools

Index

A | C | D | E | F | G | J | L | M | N | O | P | R | S | T

A

  • add_shape() (lmd.lib.Collection method)

C

  • calibration_points (lmd.lib.Collection attribute)
  • check_cell_set_sanity() (lmd.lib.SegmentationLoader method)
  • Collection (class in lmd.lib)

D

  • DEFAULT_SEGMENTATION_DTYPE (lmd.lib.SegmentationLoader attribute)

E

  • ellipse() (in module lmd.tools)

F

  • from_xml() (lmd.lib.Shape class method)

G

  • get_shape_annotation() (lmd.lib.Shape method)
  • glyph() (in module lmd.tools)
  • glyph_path() (in module lmd.tools)

J

  • join() (lmd.lib.Collection method)

L

  • lmd.lib
    • module
  • lmd.tools
    • module
  • load() (lmd.lib.Collection method)
  • load_classes() (lmd.lib.SegmentationLoader method)
  • load_geopandas() (lmd.lib.Collection method)

M

  • makeCross() (in module lmd.tools)
  • module
    • lmd.lib
    • lmd.tools

N

  • new_shape() (lmd.lib.Collection method)

O

  • orientation_transform (lmd.lib.Collection attribute)

P

  • plot() (lmd.lib.Collection method)

R

  • rectangle() (in module lmd.tools)

S

  • save() (lmd.lib.Collection method)
  • SegmentationLoader (class in lmd.lib)
  • Shape (class in lmd.lib)
  • shapes (lmd.lib.Collection attribute)
  • stats() (lmd.lib.Collection method)
  • svg_to_lmd() (lmd.lib.Collection method)

T

  • text() (in module lmd.tools)
  • to_geopandas() (lmd.lib.Collection method)
  • to_xml() (lmd.lib.Shape method)

By Georg Wallmann, Sophia Mädler and Niklas Schmacke

© Copyright 2023 Georg Wallmann, Sophia Mädler and Niklas Schmacke.