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)
Project details
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ndx-fret-0.2.1.tar.gz
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