Index

Symbols

0() (playnano.analysis.modules.log_blob_detection.LoGBlobDetectionModule.0.1 method)

A

add() (playnano.analysis.pipeline.AnalysisPipeline method) add_filter() (playnano.processing.pipeline.ProcessingPipeline method) add_mask() (playnano.processing.pipeline.ProcessingPipeline method) AFMImageStack (class in playnano.afm_stack) align_frames() (in module playnano.processing.video_processing) analysis (playnano.afm_stack.AFMImageStack attribute)

AnalysisModule (class in playnano.analysis.base) AnalysisPipeline (class in playnano.analysis.pipeline) AnalysisRecord (in module playnano.analysis.pipeline) apply() (playnano.afm_stack.AFMImageStack method) apply_z_unit_conversion() (in module playnano.io.formats.read_h5jpk) ask_for_analysis_params() (in module playnano.cli.utils) ask_for_processing_params() (in module playnano.cli.utils)

C

channel (playnano.afm_stack.AFMImageStack attribute) channel_for_frame() (playnano.afm_stack.AFMImageStack method) check_path_is_path() (in module playnano.io.export_data) clear() (playnano.analysis.pipeline.AnalysisPipeline method) clear_mask() (playnano.processing.pipeline.ProcessingPipeline method)

compute_bic() (in module playnano.analysis.modules.x_means_clustering) core_xmeans() (in module playnano.analysis.modules.x_means_clustering) CountNonzeroModule (class in playnano.analysis.modules.count_nonzero) create_gif_with_scale_and_timestamp() (in module playnano.io.gif_export) crop_square() (in module playnano.processing.video_processing)

D

data (playnano.afm_stack.AFMImageStack attribute) DBSCANClusteringModule (class in playnano.analysis.modules.dbscan_clustering)

default() (playnano.analysis.utils.common.NumpyEncoder method) drop_frame_range() (in module playnano.processing.stack_edit) drop_frames() (in module playnano.processing.stack_edit)

E

export_analysis_log() (playnano.afm_stack.AFMImageStack method) export_analysis_to_json() (in module playnano.analysis.export) export_bundles() (in module playnano.io.export_data)

export_gif() (in module playnano.io.gif_export) export_particle_csv() (in module playnano.analysis.utils.particles) export_processing_log() (playnano.afm_stack.AFMImageStack method) export_to_hdf5() (in module playnano.analysis.utils.common)

F

FeatureDetectionModule (class in playnano.analysis.modules.feature_detection) file_path (playnano.afm_stack.AFMImageStack attribute) flatten_particle_features() (in module playnano.analysis.utils.particles)

frame_metadata (playnano.afm_stack.AFMImageStack attribute) frame_summary_to_dataframe() (in module playnano.analysis.utils.frames) frames_with_metadata() (playnano.afm_stack.AFMImageStack method)

G

gaussian_filter() (in module playnano.processing.filters) get_frame() (playnano.afm_stack.AFMImageStack method) get_frame_metadata() (playnano.afm_stack.AFMImageStack method) get_frame_times() (playnano.afm_stack.AFMImageStack method)

get_frames() (playnano.afm_stack.AFMImageStack method) get_loader_for_file() (in module playnano.io.loader) get_loader_for_folder() (in module playnano.io.loader) get_processing_step_type() (in module playnano.cli.utils)

H

height (playnano.afm_stack.AFMImageStack property)

I

image_shape (playnano.afm_stack.AFMImageStack property) initialize_centers() (in module playnano.analysis.modules.x_means_clustering)

intersection_crop() (in module playnano.processing.video_processing) is_valid_analysis_step() (in module playnano.cli.utils) is_valid_step() (in module playnano.cli.utils)

K

KMeansClusteringModule (class in playnano.analysis.modules.k_means_clustering)

L

load_afm_stack() (in module playnano.io.loader) load_analysis_from_hdf5() (in module playnano.analysis.utils.common) load_analysis_module() (in module playnano.analysis.utils.loader) load_asd_file() (in module playnano.io.formats.read_asd) load_data() (playnano.afm_stack.AFMImageStack class method) load_h5_bundle() (in module playnano.io.data_loaders)

load_h5jpk() (in module playnano.io.formats.read_h5jpk) load_jpk_folder() (in module playnano.io.formats.read_jpk_folder) load_npz_bundle() (in module playnano.io.data_loaders) load_ome_tiff_stack() (in module playnano.io.data_loaders) load_spm_folder() (in module playnano.io.formats.read_spm_folder) LoadError LoGBlobDetectionModule (class in playnano.analysis.modules.log_blob_detection)

M

make_json_safe() (in module playnano.analysis.utils.common) mask_adaptive() (in module playnano.processing.mask_generators) mask_below_threshold() (in module playnano.processing.mask_generators) mask_mean_offset() (in module playnano.processing.mask_generators) mask_morphological() (in module playnano.processing.mask_generators) mask_threshold() (in module playnano.processing.mask_generators) masks (playnano.afm_stack.AFMImageStack attribute) module playnano playnano.afm_stack playnano.analysis playnano.analysis.base playnano.analysis.export playnano.analysis.modules playnano.analysis.modules.count_nonzero playnano.analysis.modules.dbscan_clustering playnano.analysis.modules.feature_detection playnano.analysis.modules.k_means_clustering playnano.analysis.modules.log_blob_detection playnano.analysis.modules.particle_tracking playnano.analysis.modules.x_means_clustering playnano.analysis.pipeline playnano.analysis.utils playnano.analysis.utils.common playnano.analysis.utils.frames playnano.analysis.utils.loader playnano.analysis.utils.particles playnano.cli playnano.cli.utils playnano.errors playnano.gui playnano.gui.widgets playnano.io playnano.io.data_loaders playnano.io.export_data playnano.io.formats playnano.io.formats.read_asd playnano.io.formats.read_h5jpk playnano.io.formats.read_jpk_folder playnano.io.formats.read_spm_folder playnano.io.gif_export playnano.io.loader playnano.processing playnano.processing.core playnano.processing.filters playnano.processing.mask_generators playnano.processing.masked_filters playnano.processing.pipeline playnano.processing.stack_edit playnano.processing.video_processing

N

n_frames (playnano.afm_stack.AFMImageStack property) name (playnano.analysis.base.AnalysisModule property) (playnano.analysis.modules.count_nonzero.CountNonzeroModule property) (playnano.analysis.modules.dbscan_clustering.DBSCANClusteringModule property) (playnano.analysis.modules.feature_detection.FeatureDetectionModule property) (playnano.analysis.modules.k_means_clustering.KMeansClusteringModule property) (playnano.analysis.modules.log_blob_detection.LoGBlobDetectionModule property) (playnano.analysis.modules.particle_tracking.ParticleTrackingModule property) (playnano.analysis.modules.x_means_clustering.XMeansClusteringModule property)

NumpyEncoder (class in playnano.analysis.utils.common)

P

parse_analysis_file() (in module playnano.cli.utils) parse_analysis_string() (in module playnano.cli.utils) parse_processing_file() (in module playnano.cli.utils) parse_processing_string() (in module playnano.cli.utils) parse_spm_header() (in module playnano.io.formats.read_spm_folder) ParticleTrackingModule (class in playnano.analysis.modules.particle_tracking) pixel_size_nm (playnano.afm_stack.AFMImageStack attribute) playnano module playnano.afm_stack module playnano.analysis module playnano.analysis.base module playnano.analysis.export module playnano.analysis.modules module playnano.analysis.modules.count_nonzero module playnano.analysis.modules.dbscan_clustering module playnano.analysis.modules.feature_detection module playnano.analysis.modules.k_means_clustering module playnano.analysis.modules.log_blob_detection module playnano.analysis.modules.particle_tracking module playnano.analysis.modules.x_means_clustering module playnano.analysis.pipeline module playnano.analysis.utils module playnano.analysis.utils.common module playnano.analysis.utils.frames module playnano.analysis.utils.loader module playnano.analysis.utils.particles module playnano.cli module playnano.cli.utils module

playnano.errors module playnano.gui module playnano.gui.widgets module playnano.io module playnano.io.data_loaders module playnano.io.export_data module playnano.io.formats module playnano.io.formats.read_asd module playnano.io.formats.read_h5jpk module playnano.io.formats.read_jpk_folder module playnano.io.formats.read_spm_folder module playnano.io.gif_export module playnano.io.loader module playnano.processing module playnano.processing.core module playnano.processing.filters module playnano.processing.mask_generators module playnano.processing.masked_filters module playnano.processing.pipeline module playnano.processing.stack_edit module playnano.processing.video_processing module plot_frame_histogram() (in module playnano.analysis.utils.frames) plot_particle_labels_3d() (in module playnano.analysis.utils.particles) polynomial_flatten() (in module playnano.processing.filters) polynomial_flatten_masked() (in module playnano.processing.masked_filters) process_stack() (in module playnano.processing.core) processed (playnano.afm_stack.AFMImageStack attribute) ProcessingPipeline (class in playnano.processing.pipeline) provenance (playnano.afm_stack.AFMImageStack attribute)

R

register_filters() (in module playnano.processing.filters) register_mask_filters() (in module playnano.processing.masked_filters) register_masking() (in module playnano.processing.mask_generators) register_stack_edit_processing() (in module playnano.processing.stack_edit) register_video_processing() (in module playnano.processing.video_processing) remove_plane() (in module playnano.processing.filters) remove_plane_masked() (in module playnano.processing.masked_filters) replace_nan() (in module playnano.processing.video_processing) requires (playnano.analysis.modules.dbscan_clustering.DBSCANClusteringModule attribute) (playnano.analysis.modules.k_means_clustering.KMeansClusteringModule attribute) (playnano.analysis.modules.particle_tracking.ParticleTrackingModule attribute) (playnano.analysis.modules.x_means_clustering.XMeansClusteringModule attribute) restore_frame_metadata() (playnano.afm_stack.AFMImageStack method)

restore_raw() (playnano.afm_stack.AFMImageStack method) rolling_frame_align() (in module playnano.processing.video_processing) row_median_align() (in module playnano.processing.filters) row_median_align_masked() (in module playnano.processing.masked_filters) run() (playnano.analysis.base.AnalysisModule method) (playnano.analysis.modules.count_nonzero.CountNonzeroModule method) (playnano.analysis.modules.dbscan_clustering.DBSCANClusteringModule method) (playnano.analysis.modules.feature_detection.FeatureDetectionModule method) (playnano.analysis.modules.k_means_clustering.KMeansClusteringModule method) (playnano.analysis.modules.log_blob_detection.LoGBlobDetectionModule method) (playnano.analysis.modules.particle_tracking.ParticleTrackingModule method) (playnano.analysis.modules.x_means_clustering.XMeansClusteringModule method) (playnano.analysis.pipeline.AnalysisPipeline method) (playnano.processing.pipeline.ProcessingPipeline method)

S

safe_json_dumps() (in module playnano.analysis.utils.common) sanitize_analysis_for_logging() (in module playnano.analysis.utils.common) save_h5_bundle() (in module playnano.io.export_data)

save_npz_bundle() (in module playnano.io.export_data) save_ome_tiff_stack() (in module playnano.io.export_data) select_frames() (in module playnano.processing.stack_edit)

T

temporal_mean_filter() (in module playnano.processing.video_processing)

temporal_median_filter() (in module playnano.processing.video_processing) time_for_frame() (playnano.afm_stack.AFMImageStack method)

V

version (playnano.analysis.modules.count_nonzero.CountNonzeroModule attribute) (playnano.analysis.modules.dbscan_clustering.DBSCANClusteringModule attribute) (playnano.analysis.modules.feature_detection.FeatureDetectionModule attribute) (playnano.analysis.modules.k_means_clustering.KMeansClusteringModule attribute) (playnano.analysis.modules.log_blob_detection.LoGBlobDetectionModule attribute) (playnano.analysis.modules.particle_tracking.ParticleTrackingModule attribute) (playnano.analysis.modules.x_means_clustering.XMeansClusteringModule attribute)

Version() (playnano.analysis.modules.log_blob_detection.LoGBlobDetectionModule method)

W

width (playnano.afm_stack.AFMImageStack property)

X

XMeansClusteringModule (class in playnano.analysis.modules.x_means_clustering)

Z

zero_mean() (in module playnano.processing.filters)

zero_mean_masked() (in module playnano.processing.masked_filters)