Index

_

__init__() (multiScaleAnalysis.SegmentationHighres.Merge_ConnectedComponents_Cellpose.merge_segmentations method) (multiScaleAnalysis.SegmentationHighres.preprocessing_class.ImagePreprocessing method) (multiScaleAnalysis.SegmentationLowres.segment_lowres_3d_stitched.segment_macrophage_lowres_class method) (multiScaleAnalysis.Stitching.multiScale_stitching.image_stitcher method) (multiScaleAnalysis.Visualization.visualize_stitched_lowres.image_visualizer_stitched method) (multiScaleAnalysis.Visualization.visualize_with_napariHighRes_A375.image_visualizer method) (multiScaleAnalysis.Visualization.visualize_with_napariHighRes_MDAMB231.image_visualizer method) (multiScaleAnalysis.Visualization.visualize_with_napariHighRes_MDAMB231_2.image_visualizer method) (multiScaleAnalysis.Visualization.visualize_with_napariHighRes_nuclei_histones.image_visualizer2 method) (multiScaleAnalysis.Visualization.visualize_with_napariHighRes_spheroids.image_visualizer method) (multiScaleAnalysis.Visualization.visualize_with_napariHighRes_U2OS.image_visualizer method) (multiScaleAnalysis.Visualization.visualize_with_napariHighRes_U2OS_segmentation.image_visualizer method) (multiScaleAnalysis.Visualization.visualize_with_napariLowRes_MDAMB231.image_visualizer method) (multiScaleAnalysis.Visualization.visualize_with_napariLowRes_nuclei.image_visualizer method) (multiScaleAnalysis.Visualization.visualize_with_napariLowRes_spheroids.image_visualizer method)

A

anisodiff() (in module multiScaleAnalysis.SegmentationHighres.gradient_watershed.filters) (multiScaleAnalysis.SegmentationHighres.preprocessing_class.ImagePreprocessing method)

apply_cellpose_model_2D_prob() (in module multiScaleAnalysis.SegmentationHighres.gradient_watershed.segmentation) apply_unmix_model() (multiScaleAnalysis.SegmentationHighres.preprocessing_class.ImagePreprocessing method)

B

binarize_label_image() (in module multiScaleAnalysis.Tools.PSF_measurements)

C

cellpose_diffuse2D() (in module multiScaleAnalysis.SegmentationHighres.gradient_watershed.flows) (in module multiScaleAnalysis.SegmentationHighres.gradient_watershed.flows_backup) compute_metrics_cells() (in module multiScaleAnalysis.SegmentationHighres.gradient_watershed.metrics) connected_components_pts_2D() (in module multiScaleAnalysis.SegmentationHighres.gradient_watershed.watershed) (in module multiScaleAnalysis.SegmentationHighres.gradient_watershed.watershed_backup)

connected_components_pts_3D() (in module multiScaleAnalysis.SegmentationHighres.gradient_watershed.watershed) (in module multiScaleAnalysis.SegmentationHighres.gradient_watershed.watershed_backup) crop_images() (multiScaleAnalysis.Stitching.multiScale_stitching.image_stitcher method)

D

demix_videos() (multiScaleAnalysis.SegmentationHighres.preprocessing_class.ImagePreprocessing method) determinePSFvalues() (in module multiScaleAnalysis.Tools.PSF_measurements) diffuse_labels3D() (in module multiScaleAnalysis.SegmentationHighres.gradient_watershed.filters) distance_centroid_tform_flow_labels2D() (in module multiScaleAnalysis.SegmentationHighres.gradient_watershed.flows) (in module multiScaleAnalysis.SegmentationHighres.gradient_watershed.flows_backup) distance_centroid_tform_flow_labels2D_dask() (in module multiScaleAnalysis.SegmentationHighres.gradient_watershed.flows) distance_centroid_tform_flow_labels2D_parallel() (in module multiScaleAnalysis.SegmentationHighres.gradient_watershed.flows) (in module multiScaleAnalysis.SegmentationHighres.gradient_watershed.flows_backup)

distance_tform_labels2D() (in module multiScaleAnalysis.SegmentationHighres.gradient_watershed.flows) (in module multiScaleAnalysis.SegmentationHighres.gradient_watershed.flows_backup) distance_tform_labels2D_parallel() (in module multiScaleAnalysis.SegmentationHighres.gradient_watershed.flows) (in module multiScaleAnalysis.SegmentationHighres.gradient_watershed.flows_backup) distance_transform_labels_fast() (in module multiScaleAnalysis.SegmentationHighres.gradient_watershed.flows) (in module multiScaleAnalysis.SegmentationHighres.gradient_watershed.flows_backup)

E

entropy_mean() (in module multiScaleAnalysis.SegmentationHighres.gradient_watershed.filters)

expand_masks() (in module multiScaleAnalysis.SegmentationHighres.gradient_watershed.filters) expand_masks2D() (in module multiScaleAnalysis.SegmentationHighres.gradient_watershed.filters)

F

fast_normalized_dct_shannon_entropy() (in module multiScaleAnalysis.Tools.ShannonEntropyAnalysis) filter_centroidpositions() (in module multiScaleAnalysis.Tools.PSF_measurements) filter_psfvalues() (in module multiScaleAnalysis.Tools.PSF_measurements)

filter_segmentations_axis() (in module multiScaleAnalysis.SegmentationHighres.gradient_watershed.filters) filter_segmentations_axis_IoU() (in module multiScaleAnalysis.SegmentationHighres.gradient_watershed.filters) fmm_point_source2D() (in module multiScaleAnalysis.SegmentationHighres.gradient_watershed.flows) (in module multiScaleAnalysis.SegmentationHighres.gradient_watershed.flows_backup)

G

Gauss() (in module multiScaleAnalysis.Tools.PSF_measurements) generate2Dsegmentations() (in module multiScaleAnalysis.SegmentationHighres.Cellpose_based_MacrophageSegmentation) generate_binaryimage() (in module multiScaleAnalysis.SegmentationHighres.Cellpose_based_MacrophageSegmentation) (in module multiScaleAnalysis.SegmentationHighres.ConnectedComponent_MacrophageSegmentation) get_centroidpositions() (in module multiScaleAnalysis.Tools.PSF_measurements) get_colors() (in module multiScaleAnalysis.SegmentationHighres.gradient_watershed.plotting)

get_psfvalues() (in module multiScaleAnalysis.Tools.PSF_measurements) give_label_new_identiyinarea() (multiScaleAnalysis.SegmentationHighres.Manual_curation.manual_curate_segmentation method) gradient_watershed2D_binary() (in module multiScaleAnalysis.SegmentationHighres.gradient_watershed.watershed) (in module multiScaleAnalysis.SegmentationHighres.gradient_watershed.watershed_backup) gradient_watershed3D_binary() (in module multiScaleAnalysis.SegmentationHighres.gradient_watershed.watershed) (in module multiScaleAnalysis.SegmentationHighres.gradient_watershed.watershed_backup) gradient_watershed3D_binary_dynamics() (in module multiScaleAnalysis.SegmentationHighres.gradient_watershed.watershed)

I

image_stitcher (class in multiScaleAnalysis.Stitching.multiScale_stitching) image_visualizer (class in multiScaleAnalysis.Visualization.visualize_with_napariHighRes_A375) (class in multiScaleAnalysis.Visualization.visualize_with_napariHighRes_MDAMB231) (class in multiScaleAnalysis.Visualization.visualize_with_napariHighRes_MDAMB231_2) (class in multiScaleAnalysis.Visualization.visualize_with_napariHighRes_spheroids) (class in multiScaleAnalysis.Visualization.visualize_with_napariHighRes_U2OS) (class in multiScaleAnalysis.Visualization.visualize_with_napariHighRes_U2OS_segmentation) (class in multiScaleAnalysis.Visualization.visualize_with_napariLowRes_MDAMB231) (class in multiScaleAnalysis.Visualization.visualize_with_napariLowRes_nuclei) (class in multiScaleAnalysis.Visualization.visualize_with_napariLowRes_spheroids)

image_visualizer2 (class in multiScaleAnalysis.Visualization.visualize_with_napariHighRes_nuclei_histones) image_visualizer_stitched (class in multiScaleAnalysis.Visualization.visualize_stitched_lowres) ImagePreprocessing (class in multiScaleAnalysis.SegmentationHighres.preprocessing_class) iterate_overfolder() (multiScaleAnalysis.Stitching.multiScale_stitching.image_stitcher method) iterate_throughfolder() (multiScaleAnalysis.SegmentationHighres.Merge_ConnectedComponents_Cellpose.merge_segmentations method) (multiScaleAnalysis.SegmentationLowres.segment_lowres_3d_stitched.segment_macrophage_lowres_class method)

L

largest_component_vol() (in module multiScaleAnalysis.SegmentationHighres.gradient_watershed.filters) load_image() (in module multiScaleAnalysis.Tools.PSF_measurements) (in module multiScaleAnalysis.Tools.ShannonEntropyAnalysis) (multiScaleAnalysis.Stitching.multiScale_stitching.image_stitcher method) load_images() (multiScaleAnalysis.Visualization.visualize_with_napariHighRes_A375.image_visualizer method) (multiScaleAnalysis.Visualization.visualize_with_napariHighRes_MDAMB231.image_visualizer method) (multiScaleAnalysis.Visualization.visualize_with_napariHighRes_MDAMB231_2.image_visualizer method) (multiScaleAnalysis.Visualization.visualize_with_napariHighRes_nuclei_histones.image_visualizer2 method) (multiScaleAnalysis.Visualization.visualize_with_napariHighRes_spheroids.image_visualizer method) (multiScaleAnalysis.Visualization.visualize_with_napariHighRes_U2OS.image_visualizer method) (multiScaleAnalysis.Visualization.visualize_with_napariHighRes_U2OS_segmentation.image_visualizer method) (multiScaleAnalysis.Visualization.visualize_with_napariLowRes_MDAMB231.image_visualizer method) (multiScaleAnalysis.Visualization.visualize_with_napariLowRes_nuclei.image_visualizer method) (multiScaleAnalysis.Visualization.visualize_with_napariLowRes_spheroids.image_visualizer method)

load_visualize_images() (multiScaleAnalysis.Visualization.visualize_stitched_lowres.image_visualizer_stitched method)

M

make_maxprojections() (multiScaleAnalysis.Stitching.multiScale_stitching.image_stitcher method) manual_curate_segmentation (class in multiScaleAnalysis.SegmentationHighres.Manual_curation) mean_curvature_sdf() (in module multiScaleAnalysis.SegmentationHighres.gradient_watershed.watershed) (in module multiScaleAnalysis.SegmentationHighres.gradient_watershed.watershed_backup) mean_dice_np() (in module multiScaleAnalysis.SegmentationHighres.gradient_watershed.metrics) mean_iou_np() (in module multiScaleAnalysis.SegmentationHighres.gradient_watershed.metrics) merge_label() (multiScaleAnalysis.SegmentationHighres.Manual_curation.manual_curate_segmentation method) merge_masks() (in module multiScaleAnalysis.SegmentationHighres.Cellpose_based_MacrophageSegmentation) merge_segmentations (class in multiScaleAnalysis.SegmentationHighres.Merge_ConnectedComponents_Cellpose) metrics_np() (in module multiScaleAnalysis.SegmentationHighres.gradient_watershed.metrics) mkdir() (multiScaleAnalysis.SegmentationHighres.preprocessing_class.ImagePreprocessing method) module multiScaleAnalysis multiScaleAnalysis.SegmentationHighres multiScaleAnalysis.SegmentationHighres.Cellpose_based_MacrophageSegmentation multiScaleAnalysis.SegmentationHighres.ConnectedComponent_MacrophageSegmentation multiScaleAnalysis.SegmentationHighres.gradient_watershed multiScaleAnalysis.SegmentationHighres.gradient_watershed.filters multiScaleAnalysis.SegmentationHighres.gradient_watershed.flows multiScaleAnalysis.SegmentationHighres.gradient_watershed.flows_backup multiScaleAnalysis.SegmentationHighres.gradient_watershed.metrics multiScaleAnalysis.SegmentationHighres.gradient_watershed.plotting multiScaleAnalysis.SegmentationHighres.gradient_watershed.segmentation multiScaleAnalysis.SegmentationHighres.gradient_watershed.watershed multiScaleAnalysis.SegmentationHighres.gradient_watershed.watershed_backup multiScaleAnalysis.SegmentationHighres.Manual_curation multiScaleAnalysis.SegmentationHighres.Merge_ConnectedComponents_Cellpose multiScaleAnalysis.SegmentationHighres.postprocessing_removeCancersignal multiScaleAnalysis.SegmentationHighres.preprocessing_class multiScaleAnalysis.SegmentationLowres multiScaleAnalysis.SegmentationLowres.segment_lowres_3d_stitched multiScaleAnalysis.Stitching multiScaleAnalysis.Stitching.multiScale_stitching multiScaleAnalysis.Tools multiScaleAnalysis.Tools.PSF_measurements multiScaleAnalysis.Tools.ShannonEntropyAnalysis multiScaleAnalysis.Visualization multiScaleAnalysis.Visualization.visualize_stitched_lowres multiScaleAnalysis.Visualization.visualize_with_napariHighRes_A375 multiScaleAnalysis.Visualization.visualize_with_napariHighRes_MDAMB231 multiScaleAnalysis.Visualization.visualize_with_napariHighRes_MDAMB231_2 multiScaleAnalysis.Visualization.visualize_with_napariHighRes_nuclei_histones multiScaleAnalysis.Visualization.visualize_with_napariHighRes_spheroids multiScaleAnalysis.Visualization.visualize_with_napariHighRes_U2OS multiScaleAnalysis.Visualization.visualize_with_napariHighRes_U2OS_segmentation multiScaleAnalysis.Visualization.visualize_with_napariLowRes_MDAMB231 multiScaleAnalysis.Visualization.visualize_with_napariLowRes_nuclei multiScaleAnalysis.Visualization.visualize_with_napariLowRes_spheroids multiScaleAnalysis module multiScaleAnalysis.SegmentationHighres module multiScaleAnalysis.SegmentationHighres.Cellpose_based_MacrophageSegmentation module multiScaleAnalysis.SegmentationHighres.ConnectedComponent_MacrophageSegmentation module multiScaleAnalysis.SegmentationHighres.gradient_watershed module multiScaleAnalysis.SegmentationHighres.gradient_watershed.filters module

multiScaleAnalysis.SegmentationHighres.gradient_watershed.flows module multiScaleAnalysis.SegmentationHighres.gradient_watershed.flows_backup module multiScaleAnalysis.SegmentationHighres.gradient_watershed.metrics module multiScaleAnalysis.SegmentationHighres.gradient_watershed.plotting module multiScaleAnalysis.SegmentationHighres.gradient_watershed.segmentation module multiScaleAnalysis.SegmentationHighres.gradient_watershed.watershed module multiScaleAnalysis.SegmentationHighres.gradient_watershed.watershed_backup module multiScaleAnalysis.SegmentationHighres.Manual_curation module multiScaleAnalysis.SegmentationHighres.Merge_ConnectedComponents_Cellpose module multiScaleAnalysis.SegmentationHighres.postprocessing_removeCancersignal module multiScaleAnalysis.SegmentationHighres.preprocessing_class module multiScaleAnalysis.SegmentationLowres module multiScaleAnalysis.SegmentationLowres.segment_lowres_3d_stitched module multiScaleAnalysis.Stitching module multiScaleAnalysis.Stitching.multiScale_stitching module multiScaleAnalysis.Tools module multiScaleAnalysis.Tools.PSF_measurements module multiScaleAnalysis.Tools.ShannonEntropyAnalysis module multiScaleAnalysis.Visualization module multiScaleAnalysis.Visualization.visualize_stitched_lowres module multiScaleAnalysis.Visualization.visualize_with_napariHighRes_A375 module multiScaleAnalysis.Visualization.visualize_with_napariHighRes_MDAMB231 module multiScaleAnalysis.Visualization.visualize_with_napariHighRes_MDAMB231_2 module multiScaleAnalysis.Visualization.visualize_with_napariHighRes_nuclei_histones module multiScaleAnalysis.Visualization.visualize_with_napariHighRes_spheroids module multiScaleAnalysis.Visualization.visualize_with_napariHighRes_U2OS module multiScaleAnalysis.Visualization.visualize_with_napariHighRes_U2OS_segmentation module multiScaleAnalysis.Visualization.visualize_with_napariLowRes_MDAMB231 module multiScaleAnalysis.Visualization.visualize_with_napariLowRes_nuclei module multiScaleAnalysis.Visualization.visualize_with_napariLowRes_spheroids module

N

normalize() (in module multiScaleAnalysis.SegmentationHighres.gradient_watershed.filters) (multiScaleAnalysis.SegmentationHighres.preprocessing_class.ImagePreprocessing method)

normalize99() (multiScaleAnalysis.SegmentationHighres.preprocessing_class.ImagePreprocessing method) normalize_mi_ma() (in module multiScaleAnalysis.SegmentationHighres.gradient_watershed.filters) (multiScaleAnalysis.SegmentationHighres.preprocessing_class.ImagePreprocessing method)

O

open_image() (multiScaleAnalysis.SegmentationLowres.segment_lowres_3d_stitched.segment_macrophage_lowres_class method)

optimize_overlap() (multiScaleAnalysis.Stitching.multiScale_stitching.image_stitcher method)

P

perform_2D_maximum_fusion() (multiScaleAnalysis.Stitching.multiScale_stitching.image_stitcher method) perform_2D_weighted_average_fusion() (multiScaleAnalysis.Stitching.multiScale_stitching.image_stitcher method) perform_3D_fusion() (multiScaleAnalysis.Stitching.multiScale_stitching.image_stitcher method) plot_border_tracks_2D() (in module multiScaleAnalysis.SegmentationHighres.gradient_watershed.plotting) poisson_dist_tform() (in module multiScaleAnalysis.SegmentationHighres.gradient_watershed.flows) (in module multiScaleAnalysis.SegmentationHighres.gradient_watershed.flows_backup)

poisson_dist_tform_flow() (in module multiScaleAnalysis.SegmentationHighres.gradient_watershed.flows) (in module multiScaleAnalysis.SegmentationHighres.gradient_watershed.flows_backup) prepare_segmentations() (in module multiScaleAnalysis.SegmentationHighres.ConnectedComponent_MacrophageSegmentation) process_timepoint() (multiScaleAnalysis.SegmentationHighres.Merge_ConnectedComponents_Cellpose.merge_segmentations method)

R

register_stack() (in module multiScaleAnalysis.SegmentationHighres.Cellpose_based_MacrophageSegmentation) (in module multiScaleAnalysis.SegmentationHighres.ConnectedComponent_MacrophageSegmentation) relabel_ground_truth_labels() (in module multiScaleAnalysis.SegmentationHighres.gradient_watershed.plotting) relabel_slices() (in module multiScaleAnalysis.SegmentationHighres.gradient_watershed.filters) remove_bad_flow_masks_3D() (in module multiScaleAnalysis.SegmentationHighres.gradient_watershed.flows)

remove_eccentric_shapes() (in module multiScaleAnalysis.SegmentationHighres.gradient_watershed.filters) remove_label() (multiScaleAnalysis.SegmentationHighres.Manual_curation.manual_curate_segmentation method) remove_small_labelled_objects() (in module multiScaleAnalysis.SegmentationHighres.gradient_watershed.metrics) remove_small_labels() (in module multiScaleAnalysis.SegmentationHighres.gradient_watershed.filters) remove_small_obj_and_keep_largest() (in module multiScaleAnalysis.SegmentationHighres.gradient_watershed.filters) replace_one_label() (multiScaleAnalysis.SegmentationHighres.Manual_curation.manual_curate_segmentation method)

S

saveimage() (multiScaleAnalysis.SegmentationHighres.Manual_curation.manual_curate_segmentation method) segment_cancercells() (multiScaleAnalysis.SegmentationLowres.segment_lowres_3d_stitched.segment_macrophage_lowres_class method) segment_macrophage() (multiScaleAnalysis.SegmentationLowres.segment_lowres_3d_stitched.segment_macrophage_lowres_class method) segment_macrophage_lowres_class (class in multiScaleAnalysis.SegmentationLowres.segment_lowres_3d_stitched) set_axes_equal() (in module multiScaleAnalysis.SegmentationHighres.gradient_watershed.plotting) smooth_vol() (in module multiScaleAnalysis.SegmentationHighres.gradient_watershed.filters) (multiScaleAnalysis.SegmentationHighres.preprocessing_class.ImagePreprocessing method)

smooth_vol_anisotropic() (in module multiScaleAnalysis.SegmentationHighres.gradient_watershed.filters) spectral_unmix_RGB() (multiScaleAnalysis.SegmentationHighres.preprocessing_class.ImagePreprocessing method) stitching_workflow() (multiScaleAnalysis.Stitching.multiScale_stitching.image_stitcher method) surf_normal_sdf() (in module multiScaleAnalysis.SegmentationHighres.gradient_watershed.watershed) (in module multiScaleAnalysis.SegmentationHighres.gradient_watershed.watershed_backup)

T

takeLabel_fromanotherstack() (multiScaleAnalysis.SegmentationHighres.Manual_curation.manual_curate_segmentation method)

takeLabel_fromanotherstack_range() (multiScaleAnalysis.SegmentationHighres.Manual_curation.manual_curate_segmentation method)

V

var_combine() (in module multiScaleAnalysis.SegmentationHighres.gradient_watershed.filters)

var_combine_registration() (in module multiScaleAnalysis.SegmentationHighres.gradient_watershed.filters) var_filter() (in module multiScaleAnalysis.SegmentationHighres.gradient_watershed.filters)