FRET
Project description
ndx-fret
NWB extension for storing Fluorescence Resonance Energy Transfer (FRET) experimental data. A collaboration with Jaeger Lab, Emory University and The Kavli Foundation.
Python Installation
pip install ndx-fret
Python Usage
from pynwb import NWBFile, NWBHDF5IO
from pynwb.device import Device
from pynwb.ophys import OpticalChannel
from ndx_fret import FRET, FRETSeries
from datetime import datetime
import numpy as np
nwb = NWBFile('session_description', 'identifier', datetime.now().astimezone())
# Create and add device
device = Device(name='Device')
nwb.add_device(device)
# Create optical channels
opt_ch_d = OpticalChannel(
name='optical_channel',
description='optical_channel_description',
emission_lambda=529.
)
opt_ch_a = OpticalChannel(
name='optical_channel',
description='optical_channel_description',
emission_lambda=633.
)
# Create FRET
fs_d = FRETSeries(
name='donor',
fluorophore='mCitrine',
optical_channel=opt_ch_d,
device=device,
description='description of donor series',
data=np.random.randn(100, 10, 10),
rate=200.,
unit='no unit'
)
fs_a = FRETSeries(
name='acceptor',
fluorophore='mKate2',
optical_channel=opt_ch_a,
device=device,
description='description of acceptor series',
data=np.random.randn(100, 10, 10),
rate=200.,
unit='no unit'
)
fret = FRET(
name='FRET',
excitation_lambda=482.,
donor=fs_d,
acceptor=fs_a
)
nwb.add_acquisition(fret)
# Write nwb file
with NWBHDF5IO('test_fret.nwb', 'w') as io:
io.write(nwb)
print('NWB file written')
# Read nwb file and check its content
with NWBHDF5IO('test_fret.nwb', 'r', load_namespaces=True) as io:
nwb = io.read()
print(nwb)
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