EPFL Machine Learning Course, Fall 2025

Scipy Cookbook

Notes on Scientific Computing for Biomechanics and Motor Control

code for reading and processing Allen Institute for Brain Science data

We turn natural language descriptions of behaviors into machine-executable code

Automated quality control, curation and neuron classification of spike-sorted electrophysiology data. Available in MATLAB and in Python.

A general framework for interpreting wide-band neural activity

Various scripts to support deeplabcut and what to do afterwards!

Calibrated inference of spiking from calcium ΔF/F data using deep networks

Workshop material for using DeepLabCut

a module for kinematic analysis of deeplabcut outputs

ClearMap 2 with WobblyStitcher, TubeMap and CellMap

NSCI 801 (Queen's U) Quantitative Neuroscience course materials

A napari plugin for direct 3D cell segmentation -- taking you through training, inference, and review of masks

🐕 Fun experiment to train a pose estimation model for dogs using the DeepLabCut toolkit

Camera calibration & 3D pose estimation tools for AcinoSet

Developing a Brain Atlas through Deep Learning

Docker container for running DeepLabCut 2.0, 2.1 (linux support only). Now, DLC main supports 2.2+

A sample Jupyter notebook with Binder & Colab integration

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A Primer on Motion Capture with Deep Learning:Principles, Pitfalls and Perspectives

Repository for reproducing results in Lauer et al. 2022

SuperAnimal models supporting data

CEBRA Demo Notebooks. Please see all of them at the URL below:

[Cell 2024]: Code for Task-driven neural network models predict neural dynamics of proprioception by Marin Vargas* and Bisi* et al.

Coding course materials for Brain-like computation and intelligence

DataJoint Element for behavioral analysis with DeepLabCut

[eLife 2023] Code for "Contrasting action and posture coding with hierarchical deep neural network models of proprioception"