Index

Symbols

0 (playNano.analysis.modules.particle_tracking.ParticleTrackingModule.0.1 attribute)

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) 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)

D

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

default() (playNano.analysis.utils.common.NumpyEncoder method) display_frame() (playNano.gui.widgets.viewer.ViewerWidget method)

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)

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_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.particles playNano.cli playNano.cli.actions playNano.cli.entrypoint playNano.cli.handlers playNano.cli.utils playNano.errors playNano.gui playNano.gui.main playNano.gui.widgets playNano.gui.widgets.controls playNano.gui.widgets.viewer playNano.gui.window 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.versioning

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 attribute) (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

paintEvent() (playNano.gui.widgets.viewer.ViewerWidget method) 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) PlaybackControls (class in playNano.gui.widgets.controls) 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.particles module playNano.cli module playNano.cli.actions module playNano.cli.entrypoint module playNano.cli.handlers module playNano.cli.utils module

playNano.errors module playNano.gui module playNano.gui.main module playNano.gui.widgets module playNano.gui.widgets.controls module playNano.gui.widgets.viewer module playNano.gui.window 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.versioning 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) remove_plane() (in module playNano.processing.filters) remove_plane_masked() (in module playNano.processing.masked_filters) requires (playNano.analysis.modules.dbscan_clustering.DBSCANClusteringModule attribute) (playNano.analysis.modules.k_means_clustering.KMeansClusteringModule attribute) (playNano.analysis.modules.particle_tracking.ParticleTrackingModule attribute), [1] (playNano.analysis.modules.x_means_clustering.XMeansClusteringModule attribute) resizeEvent() (playNano.gui.widgets.viewer.ViewerWidget method) restore_raw() (playNano.afm_stack.AFMImageStack method)

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) set_annotation_font() (playNano.gui.widgets.viewer.ViewerWidget method) set_annotations() (playNano.gui.widgets.viewer.ViewerWidget method) set_background_color() (playNano.gui.widgets.viewer.ViewerWidget method)

T

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)

Version (playNano.analysis.modules.particle_tracking.ParticleTrackingModule attribute) version (playNano.analysis.modules.particle_tracking.ParticleTrackingModule attribute) (playNano.analysis.modules.x_means_clustering.XMeansClusteringModule attribute) Version() (playNano.analysis.modules.log_blob_detection.LoGBlobDetectionModule method) versioned_filter() (in module playNano.processing.versioning) ViewerWidget (class in playNano.gui.widgets.viewer)

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)