Cell Painting Feature Extraction Pipeline

Getting started

  • Neurofibromatosis type 1 (NF1) 3D organoid image-based profiling pipeline
  • Python scientific stack

Features

  • Area.size.shape features
  • Colocalization features
  • Granularity features
  • Intensity features
  • Neighbors features
  • Texture features
  • SAM-med3d features
  • CHAMMI-75 features

API reference

  • API Reference
Cell Painting Feature Extraction Pipeline
  • Overview: module code

All modules for which code is available

  • image_analysis_3D.errors.exceptions
  • image_analysis_3D.featurization_utils.area_size_shape_utils
  • image_analysis_3D.featurization_utils.chammi75_featurization
  • image_analysis_3D.featurization_utils.colocalization_utils
  • image_analysis_3D.featurization_utils.errors
  • image_analysis_3D.featurization_utils.feature_writing_utils
  • image_analysis_3D.featurization_utils.granularity_utils
  • image_analysis_3D.featurization_utils.intensity_utils
  • image_analysis_3D.featurization_utils.loading_classes
  • image_analysis_3D.featurization_utils.neighbors_utils
  • image_analysis_3D.featurization_utils.resource_profiling_util
  • image_analysis_3D.featurization_utils.sammed3d_featurizer
  • image_analysis_3D.featurization_utils.texture_utils
  • image_analysis_3D.file_utils.arg_parsing_utils
  • image_analysis_3D.file_utils.file_checking
  • image_analysis_3D.file_utils.file_reading
  • image_analysis_3D.file_utils.notebook_init_utils
  • image_analysis_3D.file_utils.preprocessing_funcs
  • image_analysis_3D.file_utils.read_in_channel_mapping
  • image_analysis_3D.file_utils.segmentation_decoupling
  • image_analysis_3D.image_utils.image_utils
  • image_analysis_3D.segmentation_utils.cell_segmentation
  • image_analysis_3D.segmentation_utils.general_segmentation_utils
  • image_analysis_3D.segmentation_utils.nuclei_segmentation
  • image_analysis_3D.segmentation_utils.segmentation_decoupling
  • image_analysis_3D.visualization_utils.animation_utils

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