pykrait package

Subpackages

• pykrait.gui package
  • Submodules
  • pykrait.gui.app module
  • pykrait.gui.async_workers module
  • pykrait.gui.custom_widgets module
  • pykrait.gui.fileselection module
  • pykrait.gui.mainwindow module
  • Module contents
• pykrait.io package
  • Submodules
  • pykrait.io.files module
    • concat_analysis_files()
    • get_files_from_folder()
    • get_pykrait_version()
    • read_Txnrois()
    • save_NroisxF()
    • save_Txnrois()
  • pykrait.io.images module
    • get_pixel_contour_from_label_img()
    • load_timelapse_lazy()
    • read_image()
    • read_label_image()
  • Module contents
• pykrait.pipeline package
  • Submodules
  • pykrait.pipeline.pipeline module
    • AnalysisOutput
      • AnalysisOutput.active_cells_median_frequency_mHz
      • AnalysisOutput.analysis_folder
      • AnalysisOutput.cells_four_peaks
      • AnalysisOutput.cov_cutoff
      • AnalysisOutput.cov_quantile
      • AnalysisOutput.experiment_1st_neighbour_zscore
      • AnalysisOutput.experiment_2nd_neighbour_zscore
      • AnalysisOutput.experiment_3rd_neighbour_zscore
      • AnalysisOutput.experimental_below_cov
      • AnalysisOutput.experimental_below_std
      • AnalysisOutput.filename
      • AnalysisOutput.filepath
      • AnalysisOutput.frame_interval
      • AnalysisOutput.from_pandas()
      • AnalysisOutput.masks_path
      • AnalysisOutput.median_decay8020_s
      • AnalysisOutput.median_frequency_mHz
      • AnalysisOutput.median_peakwidth_s
      • AnalysisOutput.median_rise2080_s
      • AnalysisOutput.normalized_peaks
      • AnalysisOutput.number_of_cells
      • AnalysisOutput.number_of_frames
      • AnalysisOutput.pixel_interval_x
      • AnalysisOutput.pixel_interval_y
      • AnalysisOutput.possible_coinciding_peaks_1st_neighbour
      • AnalysisOutput.pykrait_version
      • AnalysisOutput.random_1st_neighbour_zscore
      • AnalysisOutput.random_2nd_neighbour_zscore
      • AnalysisOutput.random_3rd_neighbour_zscore
      • AnalysisOutput.random_below_cov
      • AnalysisOutput.random_below_std
      • AnalysisOutput.std_cutoff
      • AnalysisOutput.std_quantile
      • AnalysisOutput.timestamp
      • AnalysisOutput.to_pandas()
      • AnalysisOutput.total_coinciding_peaks_1st_neighbour
      • AnalysisOutput.tproj_path
    • AnalysisParameters
      • AnalysisParameters.CLAHE_normalize
      • AnalysisParameters.cellpose_model_path
      • AnalysisParameters.cov_threshold
      • AnalysisParameters.frame_interval
      • AnalysisParameters.neighbour_tolerance
      • AnalysisParameters.peak_max_width
      • AnalysisParameters.peak_min_height
      • AnalysisParameters.peak_min_width
      • AnalysisParameters.peak_prominence
      • AnalysisParameters.periodicity_method
      • AnalysisParameters.sinc_filter_window
      • AnalysisParameters.std_threshold
      • AnalysisParameters.time_window
      • AnalysisParameters.to_pandas()
      • AnalysisParameters.tproj_type
    • BatchExperiment
      • BatchExperiment.run()
    • CalciumVideo
      • CalciumVideo.run()
    • calculate_periodic_cells()
    • calculate_synchronicity()
    • create_analysis_folder()
    • create_masks()
    • create_mean_intensities()
    • create_roi_dataframe()
    • do_peak_analysis()
    • load_timelapse()
    • save_analysis_results()
    • save_params()
  • Module contents
• pykrait.preprocessing package
  • Submodules
  • pykrait.preprocessing.segmentation module
    • create_cellpose_segmentation()
    • timelapse_projection()
  • pykrait.preprocessing.timeseries_extraction module
    • extract_cell_properties()
    • extract_mean_intensities()
    • get_adjacency_matrix()
    • shrink_masks()
  • Module contents
• pykrait.trace_analysis package
  • Submodules
  • pykrait.trace_analysis.filtering module
    • detrend_with_sinc_filter()
    • smooth_gauss()
  • pykrait.trace_analysis.oscillations module
    • calculate_std_cov()
    • find_median_frequency()
    • find_oscillating_rois()
    • get_random_std_covs()
  • pykrait.trace_analysis.peak_analysis module
    • calculate_normalized_peaks()
    • create_peak_properties()
    • find_peaks()
  • pykrait.trace_analysis.synchronicity module
    • calculate_synchronicity_zscore()
    • find_possible_synchronous_peaks()
    • find_synchronous_peaks()
  • Module contents
• pykrait.visualization package
  • Submodules
  • pykrait.visualization.image_overlays module
    • compute_offset_lines()
    • create_heatmap_image()
    • create_synchronicity_image()
    • draw_arrow()
  • Module contents

Module contents