Index

A

active_cells_median_frequency_mHz (pykrait.pipeline.pipeline.AnalysisOutput attribute) analysis_folder (pykrait.pipeline.pipeline.AnalysisOutput attribute)

AnalysisOutput (class in pykrait.pipeline.pipeline) AnalysisParameters (class in pykrait.pipeline.pipeline)

B

BatchExperiment (class in pykrait.pipeline.pipeline)

C

CalciumVideo (class in pykrait.pipeline.pipeline) calculate_normalized_peaks() (in module pykrait.trace_analysis.peak_analysis) calculate_periodic_cells() (in module pykrait.pipeline.pipeline) calculate_std_cov() (in module pykrait.trace_analysis.oscillations) calculate_synchronicity() (in module pykrait.pipeline.pipeline) calculate_synchronicity_zscore() (in module pykrait.trace_analysis.synchronicity) cellpose_model_path (pykrait.pipeline.pipeline.AnalysisParameters attribute) cells_four_peaks (pykrait.pipeline.pipeline.AnalysisOutput attribute) CLAHE_normalize (pykrait.pipeline.pipeline.AnalysisParameters attribute) compute_offset_lines() (in module pykrait.visualization.image_overlays) concat_analysis_files() (in module pykrait.io.files)

cov_cutoff (pykrait.pipeline.pipeline.AnalysisOutput attribute) cov_quantile (pykrait.pipeline.pipeline.AnalysisOutput attribute) cov_threshold (pykrait.pipeline.pipeline.AnalysisParameters attribute) create_analysis_folder() (in module pykrait.pipeline.pipeline) create_cellpose_segmentation() (in module pykrait.preprocessing.segmentation) create_heatmap_image() (in module pykrait.visualization.image_overlays) create_masks() (in module pykrait.pipeline.pipeline) create_mean_intensities() (in module pykrait.pipeline.pipeline) create_peak_properties() (in module pykrait.trace_analysis.peak_analysis) create_roi_dataframe() (in module pykrait.pipeline.pipeline) create_synchronicity_image() (in module pykrait.visualization.image_overlays)

D

detrend_with_sinc_filter() (in module pykrait.trace_analysis.filtering)

do_peak_analysis() (in module pykrait.pipeline.pipeline) draw_arrow() (in module pykrait.visualization.image_overlays)

E

experiment_1st_neighbour_zscore (pykrait.pipeline.pipeline.AnalysisOutput attribute) experiment_2nd_neighbour_zscore (pykrait.pipeline.pipeline.AnalysisOutput attribute) experiment_3rd_neighbour_zscore (pykrait.pipeline.pipeline.AnalysisOutput attribute)

experimental_below_cov (pykrait.pipeline.pipeline.AnalysisOutput attribute) experimental_below_std (pykrait.pipeline.pipeline.AnalysisOutput attribute) extract_cell_properties() (in module pykrait.preprocessing.timeseries_extraction) extract_mean_intensities() (in module pykrait.preprocessing.timeseries_extraction)

F

filename (pykrait.pipeline.pipeline.AnalysisOutput attribute) filepath (pykrait.pipeline.pipeline.AnalysisOutput attribute) find_median_frequency() (in module pykrait.trace_analysis.oscillations) find_oscillating_rois() (in module pykrait.trace_analysis.oscillations) find_peaks() (in module pykrait.trace_analysis.peak_analysis)

find_possible_synchronous_peaks() (in module pykrait.trace_analysis.synchronicity) find_synchronous_peaks() (in module pykrait.trace_analysis.synchronicity) frame_interval (pykrait.pipeline.pipeline.AnalysisOutput attribute) (pykrait.pipeline.pipeline.AnalysisParameters attribute) from_pandas() (pykrait.pipeline.pipeline.AnalysisOutput class method)

G

get_adjacency_matrix() (in module pykrait.preprocessing.timeseries_extraction) get_files_from_folder() (in module pykrait.io.files)

get_pixel_contour_from_label_img() (in module pykrait.io.images) get_pykrait_version() (in module pykrait.io.files) get_random_std_covs() (in module pykrait.trace_analysis.oscillations)

L

load_timelapse() (in module pykrait.pipeline.pipeline)

load_timelapse_lazy() (in module pykrait.io.images)

M

masks_path (pykrait.pipeline.pipeline.AnalysisOutput attribute) median_decay8020_s (pykrait.pipeline.pipeline.AnalysisOutput attribute) median_frequency_mHz (pykrait.pipeline.pipeline.AnalysisOutput attribute) median_peakwidth_s (pykrait.pipeline.pipeline.AnalysisOutput attribute) median_rise2080_s (pykrait.pipeline.pipeline.AnalysisOutput attribute) module pykrait pykrait.gui pykrait.io pykrait.io.files pykrait.io.images pykrait.pipeline pykrait.pipeline.pipeline pykrait.preprocessing pykrait.preprocessing.segmentation pykrait.preprocessing.timeseries_extraction pykrait.trace_analysis pykrait.trace_analysis.filtering pykrait.trace_analysis.oscillations pykrait.trace_analysis.peak_analysis pykrait.trace_analysis.synchronicity pykrait.visualization pykrait.visualization.image_overlays

N

neighbour_tolerance (pykrait.pipeline.pipeline.AnalysisParameters attribute) normalized_peaks (pykrait.pipeline.pipeline.AnalysisOutput attribute)

number_of_cells (pykrait.pipeline.pipeline.AnalysisOutput attribute) number_of_frames (pykrait.pipeline.pipeline.AnalysisOutput attribute)

P

peak_max_width (pykrait.pipeline.pipeline.AnalysisParameters attribute) peak_min_height (pykrait.pipeline.pipeline.AnalysisParameters attribute) peak_min_width (pykrait.pipeline.pipeline.AnalysisParameters attribute) peak_prominence (pykrait.pipeline.pipeline.AnalysisParameters attribute) periodicity_method (pykrait.pipeline.pipeline.AnalysisParameters attribute) pixel_interval_x (pykrait.pipeline.pipeline.AnalysisOutput attribute) pixel_interval_y (pykrait.pipeline.pipeline.AnalysisOutput attribute) possible_coinciding_peaks_1st_neighbour (pykrait.pipeline.pipeline.AnalysisOutput attribute) pykrait module pykrait.gui module pykrait.io module pykrait.io.files module pykrait.io.images module pykrait.pipeline module pykrait.pipeline.pipeline module

pykrait.preprocessing module pykrait.preprocessing.segmentation module pykrait.preprocessing.timeseries_extraction module pykrait.trace_analysis module pykrait.trace_analysis.filtering module pykrait.trace_analysis.oscillations module pykrait.trace_analysis.peak_analysis module pykrait.trace_analysis.synchronicity module pykrait.visualization module pykrait.visualization.image_overlays module pykrait_version (pykrait.pipeline.pipeline.AnalysisOutput attribute)

R

random_1st_neighbour_zscore (pykrait.pipeline.pipeline.AnalysisOutput attribute) random_2nd_neighbour_zscore (pykrait.pipeline.pipeline.AnalysisOutput attribute) random_3rd_neighbour_zscore (pykrait.pipeline.pipeline.AnalysisOutput attribute) random_below_cov (pykrait.pipeline.pipeline.AnalysisOutput attribute) random_below_std (pykrait.pipeline.pipeline.AnalysisOutput attribute)

read_image() (in module pykrait.io.images) read_label_image() (in module pykrait.io.images) read_Txnrois() (in module pykrait.io.files) run() (pykrait.pipeline.pipeline.BatchExperiment method) (pykrait.pipeline.pipeline.CalciumVideo method)

S

save_analysis_results() (in module pykrait.pipeline.pipeline) save_NroisxF() (in module pykrait.io.files) save_params() (in module pykrait.pipeline.pipeline) save_Txnrois() (in module pykrait.io.files) shrink_masks() (in module pykrait.preprocessing.timeseries_extraction)

sinc_filter_window (pykrait.pipeline.pipeline.AnalysisParameters attribute) smooth_gauss() (in module pykrait.trace_analysis.filtering) std_cutoff (pykrait.pipeline.pipeline.AnalysisOutput attribute) std_quantile (pykrait.pipeline.pipeline.AnalysisOutput attribute) std_threshold (pykrait.pipeline.pipeline.AnalysisParameters attribute)

T

time_window (pykrait.pipeline.pipeline.AnalysisParameters attribute) timelapse_projection() (in module pykrait.preprocessing.segmentation) timestamp (pykrait.pipeline.pipeline.AnalysisOutput attribute) to_pandas() (pykrait.pipeline.pipeline.AnalysisOutput method) (pykrait.pipeline.pipeline.AnalysisParameters method)

total_coinciding_peaks_1st_neighbour (pykrait.pipeline.pipeline.AnalysisOutput attribute) tproj_path (pykrait.pipeline.pipeline.AnalysisOutput attribute) tproj_type (pykrait.pipeline.pipeline.AnalysisParameters attribute)