8000 SimpleITK-based object classifier? · Issue #7 · haesleinhuepf/apoc · GitHub
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haesleinhuepf opened this issue Feb 6, 2022 · 1 comment
Open

SimpleITK-based object classifier? #7

haesleinhuepf opened this issue Feb 6, 2022 · 1 comment
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enhancement New feature or request

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@haesleinhuepf
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To give more options for object classification while maintaining the installability of apoc, it might make sense to setup a second ObjectClassfier, that uses internally the regionprops from SimpleITK.

We could then classify objects accorind to their

  • maximum
  • mean
  • median
  • minimum
  • sigma
  • sum
  • variance
  • bbox
  • centroid_0
  • elongation
  • feret_diameter
  • flatness
  • roundness
  • equivalent_ellipsoid_diameter_0
  • equivalent_ellipsoid_diameter_1
  • equivalent_spherical_perimeter
  • equivalent_spherical_radius
  • number_of_pixels
  • number_of_pixels_on_border
  • perimeter
  • perimeter_on_border
  • perimeter_on_border_ratio
  • principal_axes0
  • principal_axes1
  • principal_axes2
  • principal_axes3
  • principal_moments0
  • principal_moments1

We could alternatively build this in optionally in the existing object classifier. The user-interface in napari may need a major redesign for this.

See also:
https://github.com/haesleinhuepf/napari-simpleitk-image-processing/blob/main/src/napari_simpleitk_image_processing/_simpleitk_image_processing.py#L789
@haesleinhuepf haesleinhuepf added the enhancement New feature or request label Feb 6, 2022
This was referenced Feb 9, 2022
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@haesleinhuepf
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Code for this "plugin" lives in this notebook:
https://github.com/haesleinhuepf/BioImageAnalysisNotebooks/blob/main/docs/27_cell_classification/apoc_simpleitk_object_classification.ipynb

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