Note
Click here to download the full example code
This is an example of how to decode natural images from ophys traces in V1
OEID = 541206592
First, let’s download an experiment from the Allen Institute Brain Observatory
from allensdk.core.brain_observatory_cache import BrainObservatoryCache
nwb_dataset = boc.get_ophys_experiment_data(OEID)
Next, we’ll load the dF/F traces and put them in a DataFrame
timestamps, dff = nwb_dataset.get_dff_traces()
neuron_ids = nwb_dataset.get_cell_specimen_ids()
traces = pd.DataFrame(
dff.T,
columns=neuron_ids,
index=timestamps,
)
print(traces.head())
Next, we’ll load stim_table
stim_table = nwb_dataset.get_stimulus_table('natural_scenes')
print(stim_table.head())
The stim_table lists stimulus times in terms of the start and end frames of the calcium traces, but we need start times and durations for neuroglia, so we’ll need to reshape
stim_table['time'] = timestamps[stim_table['Start']]
stim_tabel['End'] = timestamps[stim_table['End']]
stim_table['duration'] = stim_tabel['End'] - stim_tabel['time']
print(stim_table.head())