DeepInterpolation-MATLAB

A MATLAB implementation of the DeepInterpolation principle.

DeepInterpolation with MATLAB

A MATLAB implementation of the DeepInterpolation principle

About DeepInterpolation

DeepInterpolation is a general-purpose algorithm used to denoise data by removing independent noise. The Allen Institute developed the principle and created a reference implementation in Python. The principle of DeepInterpolation has been published in the Nature Methods journal, with applications to systems neuroscience data.

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)	model (Dropbox, 120 MB)	sample data	👀	▶️
🧠	fMRI (functional magnetic resonance imaging)	model (Dropbox, 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.