Skip to main content

FRET

Project description

ndx-fret

PyPI version

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.,
)
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.,
)

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


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Files for ndx-fret, version 0.1.1
Filename, size File type Python version Upload date Hashes
Filename, size ndx_fret-0.1.1-py3-none-any.whl (5.1 kB) File type Wheel Python version py3 Upload date Hashes View
Filename, size ndx-fret-0.1.1.tar.gz (4.6 kB) File type Source Python version None Upload date Hashes View

Supported by

Elastic Elastic Search Pingdom Pingdom Monitoring Google Google BigQuery Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN DigiCert DigiCert EV certificate StatusPage StatusPage Status page