allensdk.brain_observatory.demixer module

allensdk.brain_observatory.demixer.demix_time_dep_masks(raw_traces, stack, masks)[source]
Parameters:
  • raw_traces – extracted traces
  • stack – movie (same length as traces)
  • masks – binary roi masks
Returns:

demixed traces

allensdk.brain_observatory.demixer.find_negative_baselines(trace)[source]
allensdk.brain_observatory.demixer.find_negative_transients_threshold(trace, window=500, length=10, std_devs=3)[source]
allensdk.brain_observatory.demixer.find_zero_baselines(traces)[source]
allensdk.brain_observatory.demixer.plot_negative_baselines(raw_traces, demix_traces, mask_array, roi_ids_mask, plot_dir, ext='png')[source]
allensdk.brain_observatory.demixer.plot_negative_transients(raw_traces, demix_traces, valid_roi, mask_array, roi_ids_mask, plot_dir, ext='png')[source]
allensdk.brain_observatory.demixer.plot_overlap_masks_lengthOne(roi_ind, masks, savefile=None, weighted=False)[source]
allensdk.brain_observatory.demixer.plot_traces(raw_trace, demix_trace, roi_id, roi_ind, save_file)[source]
allensdk.brain_observatory.demixer.plot_transients(roi_ind, t_trans, masks, traces, demix_traces, savefile)[source]
allensdk.brain_observatory.demixer.rolling_window(trace, window=500)[source]
Parameters:
  • trace
  • window
Returns: