Mouse stereotaxic trajectory planner on Allen CCFv3, with corrections so atlas depths match real animals.

Resources to display electron microscopy images of the hippocampal circuit on the office wall as a poster

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

Fourier Ring Correlation-based estimation of clearing quality

A simple GUI for automatic and manual alignment across calcium imaging sessions.

Development towards an algorithm for spike inference with autocalibration

A repository for electronics and hardware design files for a single-cell electroporation rig.

Scientific Inkscape: Inkscape extensions for figure resizing and editing

A deep learning framework for synaptic event detection

Hennestad et al. 2022

Astrocytes Semantic Segmentation

A tool for manually track neurons across days

Custom code (Python or Matlab) to compute centripetal propagation from astrocytic calcium recordings using pixel-wise correlation functions

Simple function that loads example neural data from rat hippocampal dorsal CA1 and plots it for data exploration

Open-source stereotaxic coordinator

An event-based tool for analyzing and quantifying calcium or neurotransmitter imaging data

A deep-learning-based web tool for translational and real-time pupillometry

2P cell attached recording pipeline

Code for "Cortical areas interact through a communication subspace", Semedo et al. (Neuron, 2019)

Particle Image Velocimetry tool / app. Standalone or Matlab Toolbox - free and open.

A simple Python implementation of the Hodgkin-Huxley spiking neuron model

Open Source Theremin Instrument, Arudino Codes