Loading Raw Mesoscope Imaging Data
Cellular activity recorded using a 2 photon mesoscope.
Loading raw cell detection output
Currently cell detection is done using suite2p. You can load the raw output of suite2p for loading into their GUI:
[ ]:
from one.api import ONE
one = ONE()
eid = 'b1ca324f-5db7-4106-8be2-0dd9cce17648'
FOV = 0 # The field of view (FOV) to load
suite2p_zip = one.load_dataset(eid, '*ROIData.raw', collection=f'alf/FOV_{FOV:02}')
# Unarchive zip file
import shutil
dst_dir = suite2p_zip.parent.joinpath('suite2p_output')
files = shutil.unpack_archive(suite2p_zip, dst_dir)
# Run the suite2p GUI
import suite2p.gui
suite2p.gui.run(statfile=dst_dir / 'stat.npy')
Downloading the raw images
Suite2P output vs ALF datasets
Below is a table compareing the raw output of Suite2P with the ALF datasets available through ONE.
Suite2P |
ONE |
|---|---|
F.npy [nROIs, nFrames] |
mpci.ROIActivityF.npy [nFrames, nROIs] |
Fneu.npy [nROIs, nFrames] |
mpci.ROIActivityFneu.npy [nFrames, nROIs] |
spks.npy [nROIs, nFrames] |
mpci.ROIActivityDeconvolved.npy [nFrames, nROIs] |
ops.npy (badframes) [nFrames] |
mpci.badFrames.npy [nFrames] |
iscell.npy [nROIs, 2] |
mpciROIs.included.npy [nROIs] |
stat.npy (med) [nROIs, 3] |
mpciROIs.stackPos.npy [nROIs, 3] |