allensdk.internal.brain_observatory.demixer module

allensdk.internal.brain_observatory.demixer.demix_time_dep_masks(raw_traces, stack, masks)

Parameters:

• raw_traces – extracted traces

• stack – movie (same length as traces)

• masks – binary roi masks

Returns:

demixed traces

allensdk.internal.brain_observatory.demixer.find_negative_baselines(trace)

allensdk.internal.brain_observatory.demixer.find_negative_transients_threshold(trace, window=500, length=10, std_devs=3)

allensdk.internal.brain_observatory.demixer.find_zero_baselines(traces)

allensdk.internal.brain_observatory.demixer.identify_valid_masks(mask_array)

allensdk.internal.brain_observatory.demixer.plot_negative_baselines(raw_traces, demix_traces, mask_array, roi_ids_mask, plot_dir, ext='png')

allensdk.internal.brain_observatory.demixer.plot_negative_transients(raw_traces, demix_traces, valid_roi, mask_array, roi_ids_mask, plot_dir, ext='png')

allensdk.internal.brain_observatory.demixer.plot_overlap_masks_lengthOne(roi_ind, masks, savefile=None, weighted=False)

allensdk.internal.brain_observatory.demixer.plot_traces(raw_trace, demix_trace, roi_id, roi_ind, save_file)

allensdk.internal.brain_observatory.demixer.plot_transients(roi_ind, t_trans, masks, traces, demix_traces, savefile)

allensdk.internal.brain_observatory.demixer.rolling_window(trace, window=500)

Parameters:

• trace –

• window –

Returns: