jungguchoi/deepinsight

A general framework for interpreting wide-band neural activity

DeepInsight: A general framework for interpreting wide-band neural activity

DeepInsight is a toolbox for the analysis and interpretation of wide-band neural activity and can be applied on unsorted neural data. This means the traditional step of spike-sorting can be omitted and the raw data can be used directly as input, providing a more objective way of measuring decoding performance.

Example Usage

import deepinsight

# Load your electrophysiological or calcium-imaging data
(raw_data,
 raw_timestamps,
 output,
 output_timestamps,
 info) = deepinsight.util.tetrode.read_tetrode_data(fp_raw_file)

# Transform raw data to frequency domain
deepinsight.preprocess.preprocess_input(fp_deepinsight, raw_data, sampling_rate=info['sampling_rate'],
                                        channels=info['channels'])

# Prepare outputs
deepinsight.util.tetrode.preprocess_output(fp_deepinsight, raw_timestamps, output, output_timestamps,
                                           sampling_rate=info['sampling_rate'])

# Train the model
deepinsight.train.run_from_path(fp_deepinsight, loss_functions, loss_weights)

# Get loss and shuffled loss for influence plot
losses, output_predictions, indices = deepinsight.analyse.get_model_loss(fp_deepinsight, stepsize=10)
shuffled_losses = deepinsight.analyse.get_shuffled_model_loss(fp_deepinsight, axis=1, stepsize=10)

# Plot influence across behaviours
deepinsight.visualize.plot_residuals(fp_deepinsight, frequency_spacing=2)

See also the jupyter notebook for a full example for decoding behaviours from tetrode CA1 recordings.

Following Video shows the performance of the model trained on position (left), head direction (top right) and speed (bottom right):

Installation

For now install DeepInsight with the following command:

pip install -e git+https://github.com/CYHSM/DeepInsight.git#egg=DeepInsight

A full pip installation and Colab integration will be available soon.