DeepInterpolation-MATLAB

Version 0.8.1 (160 MB) by Pradeep
A MATLAB implementation of the DeepInterpolation principle.
34 Downloads
Updated 21 May 2024
DeepInterpolation with MATLAB
A MATLAB implementation of the DeepInterpolation principle
About DeepInterpolation
DeepInterpolation is a published general-purpose algorithm created by the Allen Institute for removing noise that arrives independently from data frame to data frame.
DeepInterpolation uses deep learning to predict a data frame from the contents of several preceeding and succeeding frames. The resulting prediction is free of independent noise such as shot noise (imaging) or thermal noise (electrophysiology). If the signal is well predicted by these preeceding and succeeding frames, as in 2-photon imaging and multi-channel recording, then DeepInterpolation does an excellent job of increasing signal-to-noise ratio. In systems neuroscience, this allows more cells to be characterized with better certainty about their activity.
Getting started
Get started with inference examples using smaller datasets. You can individually view 👀 or run ▶️ each on MATLAB Online:
Inference Example
Trained Model
Sample data
View
Run
"Ephys" (electrophysiology1)
model
sample data
👀
▶️
🔬
"Ophys" (optical physiology2) object demo
model (AWS, 120 MB)
sample data
👀
▶️
🔬
"Ophys" (optical physiology2) detailed demo
model (AWS, 120 MB)
sample data
👀
▶️
🧠
fMRI (functional magnetic resonance imaging)
model (AWS, 407.55 KB)
sample_data (OpenNeuro)
👀
▶️
1 via Neuropixels neural probes
2 via two-photon (2P) calcium imaging
Requirements
Deep Learning Toolbox Converter for TensorFlow Models support package.
Going Further
Training examples
Try out training your own DeepInterpolation network. You can individually view (:eyes:) or run (:arrow_forward:) these examples on MATLAB Online:
Nickname
Model
Dataset
View
Run
"Ephys" (electrophysiology)
model
dataset
👀
▶️
"Ophys" (optical physiology)
model
dataset (AWS, 55.6 GB)
👀
(*)
(*) This data-intensive example is recommended for use on a local machine, not for MATLAB online.
Custom Datastore for DeepInterpolation
For large datasets that are too large to load entirely into memory, the custom datastore offers a solution. By initializing the datastore with a dataset's path, users can sequentially access both flanking frames and their respective center frames. This allows for easy training and inference.
For a detailed introduction and a practical workflow, see the customdatastore_example:
Nickname
Model
Dataset
View
Run
"Custom datastore" Read from a custom datastore
model
sample_data
👀
▶️
Support
DeepInterpolation with MATLAB is a public repository. Contributions can be made in the form of adding issues or submitting pull requests.
Illustration
The principle behind DeepInterpolation is illustrated in the following figure from Lecoq et al. 2021 in Nature Methods.
.
To predict the frame-of-interest ("predicted frame"), a deep learning network uses data from several preceeding and succeeding video frames. During training, the network is modified so that it produces better and better representations of the predicted frames over several datasets. During inference, the network produces predicted frames that are used in place of the original data. If the signal in the data is well predicted by the information in the preceeding and succeeding frames, then the inferred data contains a reconstruction of the original data where the usual noise that occurs independently on each frame is greatly reduced, because it is not predicted on average. The signal can be inferred with high quality in part because the network can average out the independent noise in the preceeding and succeeding frames to uncover the underlying signal just prior to and just after the signal in the predicted frame.
Uses other open source resources
We use progressbar and mimic some functions from Brain Observatory Toolbox.
Other implementations of DeepInterpolation
Python
MATLAB Release Compatibility
Created with R2023a
Compatible with any release
Platform Compatibility
Windows macOS Linux
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Version Published Release Notes
0.8.1

See release notes for this release on GitHub: https://github.com/MATLAB-Community-Toolboxes-at-INCF/DeepInterpolation-MATLAB/releases/tag/v0.8.1

0.8.0

See release notes for this release on GitHub: https://github.com/MATLAB-Community-Toolboxes-at-INCF/DeepInterpolation-MATLAB/releases/tag/v0.8.0

0.7.0

See release notes for this release on GitHub: https://github.com/MATLAB-Community-Toolboxes-at-INCF/DeepInterpolation-MATLAB/releases/tag/v0.7.0

0.6.1.0

See release notes for this release on GitHub: https://github.com/MATLAB-Community-Toolboxes-at-INCF/DeepInterpolation-MATLAB/releases/tag/v0.6.1

0.6.0.0

See release notes for this release on GitHub: https://github.com/MATLAB-Community-Toolboxes-at-INCF/DeepInterpolation-MATLAB/releases/tag/v0.6.0

0.5.0

To view or report issues in this GitHub add-on, visit the GitHub Repository.
To view or report issues in this GitHub add-on, visit the GitHub Repository.