API Reference

This first-pass API reference is generated from package docstrings. It focuses on the modules most likely to be used by notebooks, scripts, and future sitelab integration.

• celltraj.trajectory
  • Trajectory
• celltraj.features
  • featSize()
  • meanIntensity()
  • totalIntensity()
  • featZernike()
  • featHaralick()
  • boundaryFFT()
  • featBoundary()
  • featNucBoundary()
  • get_cc_cs_border()
  • boundaryCB_FFT()
  • featBoundaryCB()
  • apply3d()
  • get_contact_boundaries()
  • get_contact_labels()
  • get_neighbor_feature_map()
  • get_pca_fromdata()
• celltraj.imageprep
  • list_images()
  • organize_filelist_fov()
  • organize_filelist_time()
  • znorm()
  • histogram_stretch()
  • get_images()
  • get_tile_order()
  • get_slide_image()
  • load_ilastik()
  • get_mask_2channel_ilastik()
  • get_masks()
  • local_threshold()
  • get_labeled_mask()
  • clean_labeled_mask()
  • get_label_largestcc()
  • get_feature_map()
  • get_voronoi_masks_fromcenters()
  • make_odd()
  • get_intensity_centers()
  • save_for_viewing()
  • load_for_viewing()
  • get_voronoi_masks()
  • get_cyto_minus_nuc_labels()
  • get_cell_intensities()
  • get_registrations()
  • transform_image()
  • pad_image()
  • get_registration_expansions()
  • expand_registered_images()
  • create_h5()
  • save_frame_h5()
  • get_cell_centers()
  • get_nndist_sum()
  • get_pair_rdf_fromcenters()
  • dist_to_contact()
  • get_contactsum_dev()
  • crop_image()
• celltraj.model
  • get_transition_matrix()
  • get_transition_matrix_CG()
  • clean_clusters()
  • get_path_entropy_2point()
  • get_path_ll_2point()
  • get_kscore()
  • get_traj_ll_gmean()
  • get_H_eigs()
  • get_motifs()
  • get_landscape_coords_umap()
  • get_avdx_clusters()
  • get_kineticstates()
  • get_committor()
  • get_steady_state_matrixpowers()
  • get_kernel_sigmas()
  • get_gaussianKernelM()
  • get_koopman_eig()
  • get_koopman_modes()
  • get_koopman_inference_multiple()
  • update_mahalanobis_matrix_grad()
  • update_mahalanobis_matrix_J_old()
  • update_mahalanobis_matrix_J()
  • update_mahalanobis_matrix_flux()
• celltraj.spatial
  • get_border_dict()
  • get_surface_points()
  • get_adhesive_displacement()
  • get_surface_displacement()
  • get_surface_gradvariance()
  • get_surface_displacement_deviation()
  • get_flux_displacement()
  • get_ot_dx()
  • get_ot_displacement()
  • get_labels_fromborderdict()
  • get_volconstraint_com()
  • constrain_volume()
  • get_yukawa_force()
  • get_LJ_force()
  • get_morse_force()
  • get_secreted_ligand_density()
  • get_flux_ligdist()
  • get_border_properties()
  • get_boundary_multipole_moments()
• celltraj.translate
  • get_predictedFC()
  • get_state_decomposition()
  • get_null_correlations()
• celltraj.utilities
  • generate_xcoords_violin()
  • ternary_coords_from_3d()
  • progress_bar()
• celltraj.cli
  • main()