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colabseg 0.1 documentation

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

GUI Interactions#

Segmentation#

segmentation_gui.JupyterFramework([width, ...])

Docstring JupyterFramework for GUI

tensorvoting_wrapper.generate_tensor_voting_gui()

Controls#

py3dmol_controls.seg_visualization([width, ...])

docstring for JupyterFrontend.

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ImageIO.writeRaw

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JupyterFramework

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  • Segmentation
  • Controls
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