meanap.catnap.loader

Load suite2p output files into numpy arrays.

Functions

load_suite2p(plane0_dir)

Load all available suite2p outputs from plane0_dir.

Classes

Suite2pData([F, spks, iscell, xy_loc, fs, ...])

All arrays loaded from one suite2p/plane0 directory.
class meanap.catnap.loader.Suite2pData(F=<factory>, spks=<factory>, iscell=<factory>, xy_loc=<factory>, fs=0.0, n_frames=0, duration_s=0.0, F_denoised=None, peak_start_frames=None, peak_end_frames=None, peak_heights=None, event_areas=None, time_points=None)[source]

Bases: object

All arrays loaded from one suite2p/plane0 directory.

Parameters:

  • F (ndarray)

  • spks (ndarray)

  • iscell (ndarray)

  • xy_loc (ndarray)

  • fs (float)

  • n_frames (int)

  • duration_s (float)

  • F_denoised (ndarray | None)

  • peak_start_frames (ndarray | None)

  • peak_end_frames (ndarray | None)

  • peak_heights (ndarray | None)

  • event_areas (ndarray | None)

  • time_points (ndarray | None)

F: ndarray
property F_cells: ndarray

F for labelled cells only, shape (n_cells, n_frames).

F_denoised: ndarray | None = None
property F_denoised_cells: ndarray | None
property cell_mask: ndarray
duration_s: float = 0.0
event_areas: ndarray | None = None
fs: float = 0.0
iscell: ndarray
property n_cells: int
n_frames: int = 0
peak_end_frames: ndarray | None = None
peak_heights: ndarray | None = None
peak_start_frames: ndarray | None = None
spks: ndarray
property spks_cells: ndarray
time_points: ndarray | None = None
property xy_cells: ndarray

XY centroids for cells, shape (n_cells, 2).

xy_loc: ndarray
meanap.catnap.loader.load_suite2p(plane0_dir)[source]

Load all available suite2p outputs from plane0_dir.

Required files: F.npy, iscell.npy, stat.npy, ops.npy Optional files: spks.npy, Fdenoised.npy, peakStartFrames.npy, peakEndFrames.npy, peakHeights.npy, eventAreas.npy, timePoints.npy

Parameters:

plane0_dir (str | Path)

Return type:

Suite2pData