API reference

• Data structures
  • ColabSegData
    • ColabSegData
      • ColabSegData
      • ColabSegData.analyze_protein_membrane_min_distance
        • ColabSegData.analyze_protein_membrane_min_distance()
      • ColabSegData.backup_step_to_previous
        • ColabSegData.backup_step_to_previous()
      • ColabSegData.calculate_normals
        • ColabSegData.calculate_normals()
      • ColabSegData.compile_xyz_string
        • ColabSegData.compile_xyz_string()
      • ColabSegData.convert_tomo
        • ColabSegData.convert_tomo()
      • ColabSegData.crop_fit_around_membrane
        • ColabSegData.crop_fit_around_membrane()
      • ColabSegData.dbscan_clustering
        • ColabSegData.dbscan_clustering()
      • ColabSegData.delete_cluster
        • ColabSegData.delete_cluster()
      • ColabSegData.delete_fit
        • ColabSegData.delete_fit()
      • ColabSegData.delete_multiple_clusters
        • ColabSegData.delete_multiple_clusters()
      • ColabSegData.delete_multiple_fits
        • ColabSegData.delete_multiple_fits()
      • ColabSegData.delete_normals
        • ColabSegData.delete_normals()
      • ColabSegData.delete_protein_position
        • ColabSegData.delete_protein_position()
      • ColabSegData.eigenvalue_outlier_removal
        • ColabSegData.eigenvalue_outlier_removal()
      • ColabSegData.extract_slice
        • ColabSegData.extract_slice()
      • ColabSegData.flip_normals
        • ColabSegData.flip_normals()
      • ColabSegData.get_lamina_rotation_matrix
        • ColabSegData.get_lamina_rotation_matrix()
      • ColabSegData.get_selected_sphere_radii
        • ColabSegData.get_selected_sphere_radii()
      • ColabSegData.interpolate_membrane_closed_surface
        • ColabSegData.interpolate_membrane_closed_surface()
      • ColabSegData.interpolate_membrane_rbf
        • ColabSegData.interpolate_membrane_rbf()
      • ColabSegData.load_hdf
        • ColabSegData.load_hdf()
      • ColabSegData.load_pickle
        • ColabSegData.load_pickle()
      • ColabSegData.load_point_cloud
        • ColabSegData.load_point_cloud()
      • ColabSegData.load_protein_position
        • ColabSegData.load_protein_position()
      • ColabSegData.load_stl_file
        • ColabSegData.load_stl_file()
      • ColabSegData.load_tomogram
        • ColabSegData.load_tomogram()
      • ColabSegData.merge_clusters
        • ColabSegData.merge_clusters()
      • ColabSegData.plain_fit_and_rotate_lamina
        • ColabSegData.plain_fit_and_rotate_lamina()
      • ColabSegData.read_mrc
        • ColabSegData.read_mrc()
      • ColabSegData.reload_original_values
        • ColabSegData.reload_original_values()
      • ColabSegData.reload_previous_step
        • ColabSegData.reload_previous_step()
      • ColabSegData.save_hdf
        • ColabSegData.save_hdf()
      • ColabSegData.save_pickle
        • ColabSegData.save_pickle()
      • ColabSegData.save_values_txt
        • ColabSegData.save_values_txt()
      • ColabSegData.split_clusters
        • ColabSegData.split_clusters()
      • ColabSegData.statistical_outlier_removal
        • ColabSegData.statistical_outlier_removal()
      • ColabSegData.trim_cluster_egdes_cluster
        • ColabSegData.trim_cluster_egdes_cluster()
      • ColabSegData.trim_cluster_egdes_fit
        • ColabSegData.trim_cluster_egdes_fit()
      • ColabSegData.write_output_mrc
        • ColabSegData.write_output_mrc()
      • ColabSegData.write_txt
        • ColabSegData.write_txt()
      • ColabSegData.write_xyz
        • ColabSegData.write_xyz()
  • ImageIO
    • ImageIO
      • ImageIO
      • ImageIO.byte_order
        • ImageIO.byte_order
      • ImageIO.em
        • ImageIO.em
      • ImageIO.emByteOrderTab
        • ImageIO.emByteOrderTab
      • ImageIO.emByteOrderTabInv
        • ImageIO.emByteOrderTabInv
      • ImageIO.emDataTypeTab
        • ImageIO.emDataTypeTab
      • ImageIO.emDataTypeTabInv
        • ImageIO.emDataTypeTabInv
      • ImageIO.emDefaultHeader
        • ImageIO.emDefaultHeader
      • ImageIO.emDefaultShape
        • ImageIO.emDefaultShape
      • ImageIO.emHeaderFields
        • ImageIO.emHeaderFields
      • ImageIO.fileFormats
        • ImageIO.fileFormats
      • ImageIO.machineByteOrder
        • ImageIO.machineByteOrder
      • ImageIO.mrc
        • ImageIO.mrc
      • ImageIO.mrcDataTypeTab
        • ImageIO.mrcDataTypeTab
      • ImageIO.mrcDataTypeTabInv
        • ImageIO.mrcDataTypeTabInv
      • ImageIO.mrcDefaultHeader
        • ImageIO.mrcDefaultHeader
      • ImageIO.mrcDefaultPixel
        • ImageIO.mrcDefaultPixel
      • ImageIO.mrcDefaultShape
        • ImageIO.mrcDefaultShape
      • ImageIO.pixelsize
        • ImageIO.pixelsize
      • ImageIO.raw
        • ImageIO.raw
      • ImageIO.tiltAngle
        • ImageIO.tiltAngle
      • ImageIO.adjustLength
        • ImageIO.adjustLength()
      • ImageIO.checkFile
        • ImageIO.checkFile()
      • ImageIO.fix
        • ImageIO.fix()
      • ImageIO.fixHeader
        • ImageIO.fixHeader()
      • ImageIO.getFromEMHeader
        • ImageIO.getFromEMHeader()
      • ImageIO.getPixelsize
        • ImageIO.getPixelsize()
      • ImageIO.getTiltAngle
        • ImageIO.getTiltAngle()
      • ImageIO.parseMRCHeader
        • ImageIO.parseMRCHeader()
      • ImageIO.putInEMHeader
        • ImageIO.putInEMHeader()
      • ImageIO.read
        • ImageIO.read()
      • ImageIO.readData
        • ImageIO.readData()
      • ImageIO.readEM
        • ImageIO.readEM()
      • ImageIO.readEMHeader
        • ImageIO.readEMHeader()
      • ImageIO.readHeader
        • ImageIO.readHeader()
      • ImageIO.readMRC
        • ImageIO.readMRC()
      • ImageIO.readMRCHeader
        • ImageIO.readMRCHeader()
      • ImageIO.readRaw
        • ImageIO.readRaw()
      • ImageIO.readRawHeader
        • ImageIO.readRawHeader()
      • ImageIO.setData
        • ImageIO.setData()
      • ImageIO.setFileFormat
        • ImageIO.setFileFormat()
      • ImageIO.setTiltAngle
        • ImageIO.setTiltAngle()
      • ImageIO.write
        • ImageIO.write()
      • ImageIO.writeData
        • ImageIO.writeData()
      • ImageIO.writeEM
        • ImageIO.writeEM()
      • ImageIO.writeMRC
        • ImageIO.writeMRC()
      • ImageIO.writeRaw
        • ImageIO.writeRaw()
• GUI Interactions
  • Segmentation
    • JupyterFramework
      • JupyterFramework
      • JupyterFramework.backup_step_to_previous
        • JupyterFramework.backup_step_to_previous()
      • JupyterFramework.boot_gui
        • JupyterFramework.boot_gui()
      • JupyterFramework.calculate_and_plot_distances_proteins
        • JupyterFramework.calculate_and_plot_distances_proteins()
      • JupyterFramework.calculate_and_plot_sphere_radii
        • JupyterFramework.calculate_and_plot_sphere_radii()
      • JupyterFramework.crop_fit
        • JupyterFramework.crop_fit()
      • JupyterFramework.dbscan_recluster
        • JupyterFramework.dbscan_recluster()
      • JupyterFramework.delete_cluster
        • JupyterFramework.delete_cluster()
      • JupyterFramework.delete_fit
        • JupyterFramework.delete_fit()
      • JupyterFramework.delete_normals
        • JupyterFramework.delete_normals()
      • JupyterFramework.execute_delete_protein_positions
        • JupyterFramework.execute_delete_protein_positions()
      • JupyterFramework.execute_load_protein_position
        • JupyterFramework.execute_load_protein_position()
      • JupyterFramework.fit_cylinder
        • JupyterFramework.fit_cylinder()
      • JupyterFramework.fit_ellipsoid
        • JupyterFramework.fit_ellipsoid()
      • JupyterFramework.fit_idx_conv
        • JupyterFramework.fit_idx_conv()
      • JupyterFramework.fit_parametrization
        • JupyterFramework.fit_parametrization()
      • JupyterFramework.fit_rbf
        • JupyterFramework.fit_rbf()
      • JupyterFramework.fit_sphere
        • JupyterFramework.fit_sphere()
      • JupyterFramework.flip_normals
        • JupyterFramework.flip_normals()
      • JupyterFramework.get_and_plot_normals
        • JupyterFramework.get_and_plot_normals()
      • JupyterFramework.get_fit_normals
        • JupyterFramework.get_fit_normals()
      • JupyterFramework.gui_elements_cluster_analysis
        • JupyterFramework.gui_elements_cluster_analysis()
      • JupyterFramework.gui_elements_loading
        • JupyterFramework.gui_elements_loading()
      • JupyterFramework.highlight_clusters
        • JupyterFramework.highlight_clusters()
      • JupyterFramework.highlight_clusters_size
        • JupyterFramework.highlight_clusters_size()
      • JupyterFramework.highlight_fits
        • JupyterFramework.highlight_fits()
      • JupyterFramework.load_from_point_cloud
        • JupyterFramework.load_from_point_cloud()
      • JupyterFramework.load_from_stl_file
        • JupyterFramework.load_from_stl_file()
      • JupyterFramework.load_mrc_file
        • JupyterFramework.load_mrc_file()
      • JupyterFramework.load_pickle
        • JupyterFramework.load_pickle()
      • JupyterFramework.load_raw_image
        • JupyterFramework.load_raw_image()
      • JupyterFramework.load_state_hdf
        • JupyterFramework.load_state_hdf()
      • JupyterFramework.load_viz
        • JupyterFramework.load_viz()
      • JupyterFramework.merge_clusters
        • JupyterFramework.merge_clusters()
      • JupyterFramework.outlier_removal
        • JupyterFramework.outlier_removal()
      • JupyterFramework.plot_cluster_size
        • JupyterFramework.plot_cluster_size()
      • JupyterFramework.reload_gui
        • JupyterFramework.reload_gui()
      • JupyterFramework.remove_eigenvalue_outliers
        • JupyterFramework.remove_eigenvalue_outliers()
      • JupyterFramework.reset_input
        • JupyterFramework.reset_input()
      • JupyterFramework.rotate_back
        • JupyterFramework.rotate_back()
      • JupyterFramework.rotate_flat
        • JupyterFramework.rotate_flat()
      • JupyterFramework.sample_fit
        • JupyterFramework.sample_fit()
      • JupyterFramework.save_clusters_mrc
        • JupyterFramework.save_clusters_mrc()
      • JupyterFramework.save_clusters_txt
        • JupyterFramework.save_clusters_txt()
      • JupyterFramework.save_distance_file
        • JupyterFramework.save_distance_file()
      • JupyterFramework.save_distance_plot
        • JupyterFramework.save_distance_plot()
      • JupyterFramework.save_downcloud_txt
        • JupyterFramework.save_downcloud_txt()
      • JupyterFramework.save_normals_file
        • JupyterFramework.save_normals_file()
      • JupyterFramework.save_pickle
        • JupyterFramework.save_pickle()
      • JupyterFramework.save_radii_file
        • JupyterFramework.save_radii_file()
      • JupyterFramework.save_radii_plot
        • JupyterFramework.save_radii_plot()
      • JupyterFramework.save_state_hdf
        • JupyterFramework.save_state_hdf()
      • JupyterFramework.split_clusters
        • JupyterFramework.split_clusters()
      • JupyterFramework.trim_top_bottom
        • JupyterFramework.trim_top_bottom()
      • JupyterFramework.undo_step
        • JupyterFramework.undo_step()
      • JupyterFramework.update_downsampling
        • JupyterFramework.update_downsampling()
    • generate_tensor_voting_gui
      • generate_tensor_voting_gui
      • generate_tensor_voting_gui.reset_optimal_default_values
        • generate_tensor_voting_gui.reset_optimal_default_values()
      • generate_tensor_voting_gui.run_tv_code
        • generate_tensor_voting_gui.run_tv_code()
  • Controls
    • seg_visualization
      • seg_visualization
      • seg_visualization.add_bounding_box
        • seg_visualization.add_bounding_box()
      • seg_visualization.add_fit
        • seg_visualization.add_fit()
      • seg_visualization.add_model
        • seg_visualization.add_model()
      • seg_visualization.cluster_checkbox
        • seg_visualization.cluster_checkbox()
      • seg_visualization.delete_model
        • seg_visualization.delete_model()
      • seg_visualization.highlight_cluster
        • seg_visualization.highlight_cluster()
      • seg_visualization.highlight_clusters
        • seg_visualization.highlight_clusters()
      • seg_visualization.highlight_fits
        • seg_visualization.highlight_fits()
      • seg_visualization.load_all_models
        • seg_visualization.load_all_models()
      • seg_visualization.load_all_models_fit
        • seg_visualization.load_all_models_fit()
      • seg_visualization.load_all_models_from_file
        • seg_visualization.load_all_models_from_file()
      • seg_visualization.load_model_from_file
        • seg_visualization.load_model_from_file()
      • seg_visualization.load_normal_positions
        • seg_visualization.load_normal_positions()
      • seg_visualization.load_protein_positions
        • seg_visualization.load_protein_positions()
      • seg_visualization.make_xyz_string
        • seg_visualization.make_xyz_string()
      • seg_visualization.make_xyz_string_protein
        • seg_visualization.make_xyz_string_protein()
      • seg_visualization.removeAll
        • seg_visualization.removeAll()
      • seg_visualization.update_highlight_clusters
        • seg_visualization.update_highlight_clusters()
      • seg_visualization.update_highlight_fits
        • seg_visualization.update_highlight_fits()
      • seg_visualization.view_update
        • seg_visualization.view_update()
      • seg_visualization.view_zoomto
        • seg_visualization.view_zoomto()
• Parametrization
  • Constructor
    • Parametrization
      • Parametrization
      • Parametrization.fit
        • Parametrization.fit()
      • Parametrization.sample
        • Parametrization.sample()
  • Available Parametrizations
    • Sphere
      • Sphere
      • Sphere.compute_normal
        • Sphere.compute_normal()
      • Sphere.fit
        • Sphere.fit()
      • Sphere.points_per_sampling
        • Sphere.points_per_sampling()
      • Sphere.sample
        • Sphere.sample()
    • Ellipsoid
      • Ellipsoid
      • Ellipsoid.compute_normal
        • Ellipsoid.compute_normal()
      • Ellipsoid.fit
        • Ellipsoid.fit()
      • Ellipsoid.points_per_sampling
        • Ellipsoid.points_per_sampling()
      • Ellipsoid.sample
        • Ellipsoid.sample()
    • Cylinder
      • Cylinder
      • Cylinder.fit
        • Cylinder.fit()
      • Cylinder.points_per_sampling
        • Cylinder.points_per_sampling()
      • Cylinder.sample
        • Cylinder.sample()
• Helpers
  • R_2vect()
  • create_sphere_points()
  • lstsq_sphere_fitting()
  • make_plot_array()
  • plane_fit()
  • ColabSegNapariWidget
    • ColabSegNapariWidget
      • ColabSegNapariWidget
      • ColabSegNapariWidget.NO_VALUE
        • ColabSegNapariWidget.NO_VALUE
      • ColabSegNapariWidget.annotation
        • ColabSegNapariWidget.annotation
      • ColabSegNapariWidget.changed
        • ColabSegNapariWidget.changed
      • ColabSegNapariWidget.enabled
        • ColabSegNapariWidget.enabled
      • ColabSegNapariWidget.height
        • ColabSegNapariWidget.height
      • ColabSegNapariWidget.label
        • ColabSegNapariWidget.label
      • ColabSegNapariWidget.label_changed
        • ColabSegNapariWidget.label_changed
      • ColabSegNapariWidget.labels
        • ColabSegNapariWidget.labels
      • ColabSegNapariWidget.layout
        • ColabSegNapariWidget.layout
      • ColabSegNapariWidget.margins
        • ColabSegNapariWidget.margins
      • ColabSegNapariWidget.max_height
        • ColabSegNapariWidget.max_height
      • ColabSegNapariWidget.max_width
        • ColabSegNapariWidget.max_width
      • ColabSegNapariWidget.min_height
        • ColabSegNapariWidget.min_height
      • ColabSegNapariWidget.min_width
        • ColabSegNapariWidget.min_width
      • ColabSegNapariWidget.native
        • ColabSegNapariWidget.native
      • ColabSegNapariWidget.native_parent_changed
        • ColabSegNapariWidget.native_parent_changed
      • ColabSegNapariWidget.options
        • ColabSegNapariWidget.options
      • ColabSegNapariWidget.orientation
        • ColabSegNapariWidget.orientation
      • ColabSegNapariWidget.param_kind
        • ColabSegNapariWidget.param_kind
      • ColabSegNapariWidget.parent
        • ColabSegNapariWidget.parent
      • ColabSegNapariWidget.parent_changed
        • ColabSegNapariWidget.parent_changed
      • ColabSegNapariWidget.root_native_widget
        • ColabSegNapariWidget.root_native_widget
      • ColabSegNapariWidget.tooltip
        • ColabSegNapariWidget.tooltip
      • ColabSegNapariWidget.visible
        • ColabSegNapariWidget.visible
      • ColabSegNapariWidget.widget_type
        • ColabSegNapariWidget.widget_type
      • ColabSegNapariWidget.width
        • ColabSegNapariWidget.width
      • ColabSegNapariWidget.append
        • ColabSegNapariWidget.append()
      • ColabSegNapariWidget.asdict
        • ColabSegNapariWidget.asdict()
      • ColabSegNapariWidget.clear
        • ColabSegNapariWidget.clear()
      • ColabSegNapariWidget.close
        • ColabSegNapariWidget.close()
      • ColabSegNapariWidget.count
        • ColabSegNapariWidget.count()
      • ColabSegNapariWidget.export_data
        • ColabSegNapariWidget.export_data()
      • ColabSegNapariWidget.extend
        • ColabSegNapariWidget.extend()
      • ColabSegNapariWidget.from_callable
        • ColabSegNapariWidget.from_callable()
      • ColabSegNapariWidget.from_signature
        • ColabSegNapariWidget.from_signature()
      • ColabSegNapariWidget.hide
        • ColabSegNapariWidget.hide()
      • ColabSegNapariWidget.index
        • ColabSegNapariWidget.index()
      • ColabSegNapariWidget.insert
        • ColabSegNapariWidget.insert()
      • ColabSegNapariWidget.load_data
        • ColabSegNapariWidget.load_data()
      • ColabSegNapariWidget.pop
        • ColabSegNapariWidget.pop()
      • ColabSegNapariWidget.remove
        • ColabSegNapariWidget.remove()
      • ColabSegNapariWidget.render
        • ColabSegNapariWidget.render()
      • ColabSegNapariWidget.reset_choices
        • ColabSegNapariWidget.reset_choices()
      • ColabSegNapariWidget.reverse
        • ColabSegNapariWidget.reverse()
      • ColabSegNapariWidget.show
        • ColabSegNapariWidget.show()
      • ColabSegNapariWidget.shown
        • ColabSegNapariWidget.shown()
      • ColabSegNapariWidget.update
        • ColabSegNapariWidget.update()
  • NapariManager
    • NapariManager
      • NapariManager
      • NapariManager.close
        • NapariManager.close()
      • NapariManager.export_data
        • NapariManager.export_data()
      • NapariManager.run
        • NapariManager.run()