Index

Symbols

0() (playnano.analysis.modules.log_blob_detection.LoGBlobDetectionModule.0.1 method), [1]

A

add() (playnano.analysis.pipeline.AnalysisPipeline method), [1] add_filter() (playnano.processing.pipeline.ProcessingPipeline method), [1] add_mask() (playnano.processing.pipeline.ProcessingPipeline method), [1] AFMImageStack (class in playnano.afm_stack), [1] align_frames() (in module playnano.processing.video_processing), [1] analysis (playnano.afm_stack.AFMImageStack attribute), [1]

AnalysisModule (class in playnano.analysis.base), [1] AnalysisPipeline (class in playnano.analysis.pipeline), [1] AnalysisRecord (in module playnano.analysis.pipeline), [1] apply() (playnano.afm_stack.AFMImageStack method), [1] apply_z_unit_conversion() (in module playnano.io.formats.read_h5jpk), [1] ask_for_analysis_params() (in module playnano.cli.utils), [1] ask_for_processing_params() (in module playnano.cli.utils), [1]

C

channel (playnano.afm_stack.AFMImageStack attribute), [1] channel_for_frame() (playnano.afm_stack.AFMImageStack method), [1] check_path_is_path() (in module playnano.io.export_data), [1] clear() (playnano.analysis.pipeline.AnalysisPipeline method), [1] clear_mask() (playnano.processing.pipeline.ProcessingPipeline method), [1]

compute_bic() (in module playnano.analysis.modules.x_means_clustering), [1] core_xmeans() (in module playnano.analysis.modules.x_means_clustering), [1] CountNonzeroModule (class in playnano.analysis.modules.count_nonzero), [1] create_gif_with_scale_and_timestamp() (in module playnano.io.gif_export), [1] crop_square() (in module playnano.processing.video_processing), [1]

D

data (playnano.afm_stack.AFMImageStack attribute), [1] DBSCANClusteringModule (class in playnano.analysis.modules.dbscan_clustering), [1]

default() (playnano.analysis.utils.common.NumpyEncoder method), [1] drop_frame_range() (in module playnano.processing.stack_edit), [1] drop_frames() (in module playnano.processing.stack_edit), [1]

E

export_analysis_log() (playnano.afm_stack.AFMImageStack method), [1] export_analysis_to_json() (in module playnano.analysis.export), [1] export_bundles() (in module playnano.io.export_data), [1]

export_gif() (in module playnano.io.gif_export), [1] export_particle_csv() (in module playnano.analysis.utils.particles), [1] export_processing_log() (playnano.afm_stack.AFMImageStack method), [1] export_to_hdf5() (in module playnano.analysis.utils.common), [1]

F

FeatureDetectionModule (class in playnano.analysis.modules.feature_detection), [1] file_path (playnano.afm_stack.AFMImageStack attribute), [1] flatten_particle_features() (in module playnano.analysis.utils.particles), [1]

frame_metadata (playnano.afm_stack.AFMImageStack attribute), [1] frame_summary_to_dataframe() (in module playnano.analysis.utils.frames), [1] frames_with_metadata() (playnano.afm_stack.AFMImageStack method), [1]

G

gaussian_filter() (in module playnano.processing.filters), [1] get_frame() (playnano.afm_stack.AFMImageStack method), [1] get_frame_metadata() (playnano.afm_stack.AFMImageStack method), [1] get_frame_times() (playnano.afm_stack.AFMImageStack method), [1]

get_frames() (playnano.afm_stack.AFMImageStack method), [1] get_loader_for_file() (in module playnano.io.loader), [1] get_loader_for_folder() (in module playnano.io.loader), [1] get_processing_step_type() (in module playnano.cli.utils), [1]

H

height (playnano.afm_stack.AFMImageStack property), [1]

I

image_shape (playnano.afm_stack.AFMImageStack property), [1] initialize_centers() (in module playnano.analysis.modules.x_means_clustering), [1]

intersection_crop() (in module playnano.processing.video_processing), [1] is_valid_analysis_step() (in module playnano.cli.utils), [1] is_valid_step() (in module playnano.cli.utils), [1]

K

KMeansClusteringModule (class in playnano.analysis.modules.k_means_clustering), [1]

L

load_afm_stack() (in module playnano.io.loader), [1] load_analysis_from_hdf5() (in module playnano.analysis.utils.common), [1] load_analysis_module() (in module playnano.analysis.utils.loader), [1] load_asd_file() (in module playnano.io.formats.read_asd), [1] load_data() (playnano.afm_stack.AFMImageStack class method), [1] load_h5_bundle() (in module playnano.io.data_loaders), [1]

load_h5jpk() (in module playnano.io.formats.read_h5jpk), [1] load_jpk_folder() (in module playnano.io.formats.read_jpk_folder), [1] load_npz_bundle() (in module playnano.io.data_loaders), [1] load_ome_tiff_stack() (in module playnano.io.data_loaders), [1] load_spm_folder() (in module playnano.io.formats.read_spm_folder), [1] LoadError, [1] LoGBlobDetectionModule (class in playnano.analysis.modules.log_blob_detection), [1]

M

make_json_safe() (in module playnano.analysis.utils.common), [1] mask_adaptive() (in module playnano.processing.mask_generators), [1] mask_below_threshold() (in module playnano.processing.mask_generators), [1] mask_mean_offset() (in module playnano.processing.mask_generators), [1] mask_morphological() (in module playnano.processing.mask_generators), [1] mask_threshold() (in module playnano.processing.mask_generators), [1] masks (playnano.afm_stack.AFMImageStack attribute), [1] module playnano playnano.afm_stack, [1] playnano.analysis playnano.analysis.base, [1] playnano.analysis.export, [1] playnano.analysis.modules playnano.analysis.modules.count_nonzero, [1] playnano.analysis.modules.dbscan_clustering, [1] playnano.analysis.modules.feature_detection, [1] playnano.analysis.modules.k_means_clustering, [1] playnano.analysis.modules.log_blob_detection, [1] playnano.analysis.modules.particle_tracking, [1] playnano.analysis.modules.x_means_clustering, [1] playnano.analysis.pipeline, [1] playnano.analysis.utils playnano.analysis.utils.common, [1] playnano.analysis.utils.frames, [1] playnano.analysis.utils.loader, [1] playnano.analysis.utils.particles, [1] playnano.cli playnano.cli.utils, [1] playnano.errors, [1] playnano.gui playnano.gui.widgets playnano.io playnano.io.data_loaders, [1] playnano.io.export_data, [1] playnano.io.formats playnano.io.formats.read_asd, [1] playnano.io.formats.read_h5jpk, [1] playnano.io.formats.read_jpk_folder, [1] playnano.io.formats.read_spm_folder, [1] playnano.io.gif_export, [1] playnano.io.loader, [1] playnano.processing playnano.processing.core, [1] playnano.processing.filters, [1] playnano.processing.mask_generators, [1] playnano.processing.masked_filters, [1] playnano.processing.pipeline, [1] playnano.processing.stack_edit, [1] playnano.processing.video_processing, [1]

N

n_frames (playnano.afm_stack.AFMImageStack property), [1] name (playnano.analysis.base.AnalysisModule property), [1] (playnano.analysis.modules.count_nonzero.CountNonzeroModule property), [1] (playnano.analysis.modules.dbscan_clustering.DBSCANClusteringModule property), [1] (playnano.analysis.modules.feature_detection.FeatureDetectionModule property), [1] (playnano.analysis.modules.k_means_clustering.KMeansClusteringModule property), [1] (playnano.analysis.modules.log_blob_detection.LoGBlobDetectionModule property), [1] (playnano.analysis.modules.particle_tracking.ParticleTrackingModule property), [1] (playnano.analysis.modules.x_means_clustering.XMeansClusteringModule property), [1]

NumpyEncoder (class in playnano.analysis.utils.common), [1]

P

parse_analysis_file() (in module playnano.cli.utils), [1] parse_analysis_string() (in module playnano.cli.utils), [1] parse_processing_file() (in module playnano.cli.utils), [1] parse_processing_string() (in module playnano.cli.utils), [1] parse_spm_header() (in module playnano.io.formats.read_spm_folder), [1] ParticleTrackingModule (class in playnano.analysis.modules.particle_tracking), [1] pixel_size_nm (playnano.afm_stack.AFMImageStack attribute), [1] playnano module playnano.afm_stack module, [1] playnano.analysis module playnano.analysis.base module, [1] playnano.analysis.export module, [1] playnano.analysis.modules module playnano.analysis.modules.count_nonzero module, [1] playnano.analysis.modules.dbscan_clustering module, [1] playnano.analysis.modules.feature_detection module, [1] playnano.analysis.modules.k_means_clustering module, [1] playnano.analysis.modules.log_blob_detection module, [1] playnano.analysis.modules.particle_tracking module, [1] playnano.analysis.modules.x_means_clustering module, [1] playnano.analysis.pipeline module, [1] playnano.analysis.utils module playnano.analysis.utils.common module, [1] playnano.analysis.utils.frames module, [1] playnano.analysis.utils.loader module, [1] playnano.analysis.utils.particles module, [1] playnano.cli module playnano.cli.utils module, [1]

playnano.errors module, [1] playnano.gui module playnano.gui.widgets module playnano.io module playnano.io.data_loaders module, [1] playnano.io.export_data module, [1] playnano.io.formats module playnano.io.formats.read_asd module, [1] playnano.io.formats.read_h5jpk module, [1] playnano.io.formats.read_jpk_folder module, [1] playnano.io.formats.read_spm_folder module, [1] playnano.io.gif_export module, [1] playnano.io.loader module, [1] playnano.processing module playnano.processing.core module, [1] playnano.processing.filters module, [1] playnano.processing.mask_generators module, [1] playnano.processing.masked_filters module, [1] playnano.processing.pipeline module, [1] playnano.processing.stack_edit module, [1] playnano.processing.video_processing module, [1] plot_frame_histogram() (in module playnano.analysis.utils.frames), [1] plot_particle_labels_3d() (in module playnano.analysis.utils.particles), [1] polynomial_flatten() (in module playnano.processing.filters), [1] polynomial_flatten_masked() (in module playnano.processing.masked_filters), [1] process_stack() (in module playnano.processing.core), [1] processed (playnano.afm_stack.AFMImageStack attribute), [1] ProcessingPipeline (class in playnano.processing.pipeline), [1] provenance (playnano.afm_stack.AFMImageStack attribute), [1]

R

register_filters() (in module playnano.processing.filters), [1] register_mask_filters() (in module playnano.processing.masked_filters), [1] register_masking() (in module playnano.processing.mask_generators), [1] register_stack_edit_processing() (in module playnano.processing.stack_edit), [1] register_video_processing() (in module playnano.processing.video_processing), [1] remove_plane() (in module playnano.processing.filters), [1] remove_plane_masked() (in module playnano.processing.masked_filters), [1] replace_nan() (in module playnano.processing.video_processing), [1] requires (playnano.analysis.modules.dbscan_clustering.DBSCANClusteringModule attribute), [1] (playnano.analysis.modules.k_means_clustering.KMeansClusteringModule attribute), [1] (playnano.analysis.modules.particle_tracking.ParticleTrackingModule attribute), [1] (playnano.analysis.modules.x_means_clustering.XMeansClusteringModule attribute), [1] restore_frame_metadata() (playnano.afm_stack.AFMImageStack method), [1]

restore_raw() (playnano.afm_stack.AFMImageStack method), [1] rolling_frame_align() (in module playnano.processing.video_processing), [1] row_median_align() (in module playnano.processing.filters), [1] row_median_align_masked() (in module playnano.processing.masked_filters), [1] run() (playnano.analysis.base.AnalysisModule method), [1] (playnano.analysis.modules.count_nonzero.CountNonzeroModule method), [1] (playnano.analysis.modules.dbscan_clustering.DBSCANClusteringModule method), [1] (playnano.analysis.modules.feature_detection.FeatureDetectionModule method), [1] (playnano.analysis.modules.k_means_clustering.KMeansClusteringModule method), [1] (playnano.analysis.modules.log_blob_detection.LoGBlobDetectionModule method), [1] (playnano.analysis.modules.particle_tracking.ParticleTrackingModule method), [1] (playnano.analysis.modules.x_means_clustering.XMeansClusteringModule method), [1] (playnano.analysis.pipeline.AnalysisPipeline method), [1] (playnano.processing.pipeline.ProcessingPipeline method), [1]

S

safe_json_dumps() (in module playnano.analysis.utils.common), [1] sanitize_analysis_for_logging() (in module playnano.analysis.utils.common), [1] save_h5_bundle() (in module playnano.io.export_data), [1]

save_npz_bundle() (in module playnano.io.export_data), [1] save_ome_tiff_stack() (in module playnano.io.export_data), [1] select_frames() (in module playnano.processing.stack_edit), [1]

T

temporal_mean_filter() (in module playnano.processing.video_processing), [1]

temporal_median_filter() (in module playnano.processing.video_processing), [1] time_for_frame() (playnano.afm_stack.AFMImageStack method), [1]

V

version (playnano.analysis.modules.count_nonzero.CountNonzeroModule attribute), [1] (playnano.analysis.modules.dbscan_clustering.DBSCANClusteringModule attribute), [1] (playnano.analysis.modules.feature_detection.FeatureDetectionModule attribute), [1] (playnano.analysis.modules.k_means_clustering.KMeansClusteringModule attribute), [1] (playnano.analysis.modules.log_blob_detection.LoGBlobDetectionModule attribute), [1] (playnano.analysis.modules.particle_tracking.ParticleTrackingModule attribute), [1] (playnano.analysis.modules.x_means_clustering.XMeansClusteringModule attribute), [1]

Version() (playnano.analysis.modules.log_blob_detection.LoGBlobDetectionModule method), [1]

W

width (playnano.afm_stack.AFMImageStack property), [1]

X

XMeansClusteringModule (class in playnano.analysis.modules.x_means_clustering), [1]

Z

zero_mean() (in module playnano.processing.filters), [1]

zero_mean_masked() (in module playnano.processing.masked_filters), [1]