Spikes

OASIS

Fast online deconvolution of calcium imaging dat

Refer to API: neuralib.spikes.oasis

See also

Example of usage

from neuralib.spikes.oasis import oasis_dcnv

# 2D dF/F array. Array[float, [nNeurons, nFrames]] or Array[float, nFrames]
dff = ...

tau = 1.5  # time constant of the calcium indicator (ms)
fs = 30  # sampling frequency of the calcium imaging data (hz)
spks = oasis_dcnv(dff, tau, fs)

Cascade

Wrapper class from Cascade to translate calcium imaging ΔF/F traces into spiking probabilities or discrete spikes

Refer to API: neuralib.spikes.cascade
tensorflow required
See available model in get_available_models()

See also

Example of usage

from neuralib.spikes.cascade import cascade_predict

# 2D dF/F array. Array[float, [nNeurons, nFrames]] or Array[float, nFrames]
dff = ...

# select your model, predict the spike probability from the dF/F (same shape)
spks = cascade_predict(dff, model_type='Global_EXC_30Hz_smoothing100ms')