ZEDprofiler

Getting started

  • ZEDprofiler
    • Install environment
    • Data Contract
    • Quality Gates

Tutorials

  • ZEDprofiler Walkthrough
    • What this walkthrough covers
    • Imports
    • Define Paths and Parameters
    • Preview Synthetic Data
    • Loading Objects and Image Sets
    • Colocalization
    • Granularity
    • Intensity
    • Neighbors
    • Texture
    • Volume, Size, and Shape
    • Merging All Features into a Single Profile
    • Normalize and Feature Select
    • Pairwise Object Correlation

Feature Schema

  • Feature schema
    • Abstract
    • 1. Introduction
      • 1.1 Purpose
      • 1.2 Scope
      • 1.3 Key words
    • 2A. feature name format specification
      • 2.1 General structure
      • 2.2 Component definitions
        • 2.2.1 Compartment component
        • 2.2.2 Channel component
        • 2.2.3 Featuretype component
        • 2.2.4 Measurement component
      • 2.3 Complete feature name examples
    • 2B. metadata naming specification
      • 2.1 General structure
      • 2.2 Metadata category definitions
      • 2.3 Complete metadata name examples
    • 3. References
      • 3.1 Normative references
      • 3.2 Informative references

Feature Modules

  • Volume.size.shape
    • Description
    • Features extracted
      • Volume.size.shape feature measurements
    • Calculation method
    • Applications
  • Colocalization
    • Description
    • Features extracted
      • Correlation-based metrics
      • Manders coefficients (M1 and M2)
      • Overlap coefficient
      • K1 and K2 coefficients
    • Use cases
  • Granularity
    • Description
    • Spectrum approach
    • Features extracted
    • Interpretation
      • High granularity at small scales (1-3):
      • High granularity at medium scales (4-8):
      • High granularity at large scales (9-16):
      • Smooth profile (low across all scales):
      • As an example, if a drug causes mitochondria to fragment, you’d see:
    • Applications
  • Intensity
    • Description
    • Features extracted
      • Location-based intensity
      • Statistical measures
      • Edge-based measurements
      • Other measurements
    • Calculation method
    • Applications
  • Neighbors
    • Description
    • Current implementation
    • Total features
    • Applications
  • Texture
    • Description
    • Calculation method
      • Parameters
    • Features extracted
      • Texture feature measurements

API reference

  • API Reference
    • Featurization utils
      • SupportsTwoObjectLoader
        • SupportsTwoObjectLoader.compartment
        • SupportsTwoObjectLoader.image1
        • SupportsTwoObjectLoader.image2
        • SupportsTwoObjectLoader.image_set_loader
        • SupportsTwoObjectLoader.label_image
        • SupportsTwoObjectLoader.object_ids
      • bisection_costes_threshold_calculation()
      • calculate_colocalization()
      • compute_colocalization()
      • linear_costes_threshold_calculation()
      • prepare_two_images_for_colocalization()
      • compute_granularity()
      • compute_intensity()
      • get_outline()
      • calculate_centroid()
      • classify_cells_into_shells()
      • compute_neighbors()
      • create_results_dataframe()
      • crop_3D_image()
      • euclidean_distance_from_centroid()
      • get_coordinates()
      • mahalanobis_distance_from_centroid()
      • neighbors_expand_box()
      • plot_distance_distributions()
      • visualize_organoid_shells()
      • compute_texture()
      • scale_image()
      • SupportsImageSetLoader
        • SupportsImageSetLoader.anisotropy_spacing
      • SupportsObjectLoader
        • SupportsObjectLoader.label_image
        • SupportsObjectLoader.object_ids
      • calculate_surface_area()
      • compute_volume_size_shape()
      • measure_3D_volume_size_shape()
    • Image utils
      • check_for_xy_squareness()
      • crop_3D_image()
      • expand_box()
      • new_crop_border()
      • select_objects_from_label()
      • single_3D_image_expand_bbox()
      • square_off_xy_crop_bbox()
    • IO utils
      • FeatureMetadata
        • FeatureMetadata.channel
        • FeatureMetadata.compartment
        • FeatureMetadata.cpu_or_gpu
        • FeatureMetadata.feature_type
      • format_morphology_feature_name()
      • remove_underscores_from_string()
      • save_features_as_parquet()
      • ImageSetConfig
        • ImageSetConfig.image_set_name
        • ImageSetConfig.label_key_name
        • ImageSetConfig.raw_image_key_name
      • ImageSetLoader
        • ImageSetLoader.image_set_name
        • ImageSetLoader.anisotropy_spacing
        • ImageSetLoader.anisotropy_factor
        • ImageSetLoader.image_set_dict
        • ImageSetLoader.unique_label_objects
        • ImageSetLoader.unique_compartment_objects
        • ImageSetLoader.image_names
        • ImageSetLoader.compartments
        • ImageSetLoader.get_anisotropy()
        • ImageSetLoader.get_compartments()
        • ImageSetLoader.get_image()
        • ImageSetLoader.get_image_names()
        • ImageSetLoader.get_unique_objects_in_compartments()
      • ObjectLoader
        • ObjectLoader.image_set_loader
        • ObjectLoader.config
        • ObjectLoader.__init__()
      • TwoObjectLoader
        • TwoObjectLoader.image_set_loader
        • TwoObjectLoader.compartment
        • TwoObjectLoader.label_image
        • TwoObjectLoader.image1
        • TwoObjectLoader.image2
        • TwoObjectLoader.object_ids
        • TwoObjectLoader.__init__()

A Note on Scalability

  • ZEDprofiler scalability
ZEDprofiler
  • Overview: module code

All modules for which code is available

  • zedprofiler.IO.feature_writing_utils
  • zedprofiler.IO.loading_classes
  • zedprofiler.featurization.colocalization
  • zedprofiler.featurization.granularity
  • zedprofiler.featurization.intensity
  • zedprofiler.featurization.neighbors
  • zedprofiler.featurization.texture
  • zedprofiler.featurization.volumesizeshape
  • zedprofiler.image_utils.image_utils

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