InscopixSegmentationExtractor#

Inscopix Segmentation Extractor.

class InscopixSegmentationExtractor(file_path: str | Path)[source]#

Bases: SegmentationExtractor

A segmentation extractor for Inscopix.

Initialize a InscopixSegmentationExtractor instance.

Main class for extracting segmentation data from Inscopix format.

Parameters:

file_path (str or Path) – The location of the folder containing Inscopix *.mat output file.

get_num_rois() → int[source]#

Get total number of Regions of Interest (ROIs) in the acquired images.

Returns:

num_rois – The number of ROIs extracted.

Return type:

int

get_roi_ids() → list[source]#

Get ROI IDs as original string IDs from the CellSet.

get_frame_shape() → tuple[int, int][source]#

Get frame size of movie (height, width).

Returns:

frame_shape – 2-D array: image height x image width

Return type:

array_like

get_accepted_list() → list[source]#

Get a list of accepted ROI ids.

Returns:

accepted_list – List of accepted ROI ids.

Return type:

list

get_rejected_list() → list[source]#

Get a list of rejected ROI ids.

Returns:

rejected_list – List of rejected ROI ids.

Return type:

list

get_traces(roi_ids=None, start_frame=None, end_frame=None, name='raw') → ndarray[source]#

Get traces for the specified ROIs.

Parameters:

  • roi_ids (list or None) – List of ROI IDs (can be integers or string IDs)

  • start_frame (int or None) – Start frame index

  • end_frame (int or None) – End frame index

  • name (str) – Name of the trace type

Returns:

Traces for the specified ROIs

Return type:

np.ndarray

get_num_samples() → int[source]#

Get the number of samples in the recording (duration of recording).

Returns:

num_samples – Number of samples in the recording.

Return type:

int

get_sampling_frequency() → float[source]#

Get the sampling frequency in Hz.

Returns:

sampling_frequency – Sampling frequency of the recording in Hz.

Return type:

float

get_native_timestamps(start_sample: int | None = None, end_sample: int | None = None) → ndarray | None[source]#

Get the original timestamps from the data source.

Parameters:

  • start_sample (int, optional) – Start sample index (inclusive).

  • end_sample (int, optional) – End sample index (exclusive).

Returns:

timestamps – The original timestamps in seconds, or None if not available.

Return type:

np.ndarray or None