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colabseg 0.1 documentation
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Quickstart
API reference
Index
GitHub
Site Navigation
Quickstart
API reference
Index
GitHub
Section Navigation
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
JupyterFramework
JupyterFrame...
JupyterFramework.load_from_stl_file
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JupyterFramework.
load_from_stl_file
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obj
)
#
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JupyterFramework.load_from_stl_file()
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