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3d_print_designs

brain-atlas

Scripts for analyzing brain atlas data (mouse for now, perhaps others later)

chronic-neuropixels-protocol

Repo requested by Cagatay Aydin (for a paper)

e6095

FFBO setup for computing with neural circuits

eeglab

EEGLAB is an open source signal processing environment for electrophysiological signals running on Matlab and developed at the SCCN/UCSD

glm-hmm

Code to reproduce figures for "Mice alternate between discrete strategies during perceptual decision-making" from Ashwood, Roy, Stone, IBL, Churchland, Pouget and Pillow (2021)

gridnext

Common coordinate registration and tissue type discovery using multimodal spatial data (ST + histology)

hash_ladder

herbs

iblpybpod

Mostly a fork of the pybpod without the git submodule structure.

iblrig

Main repository for IBL rig code

ieeg_recon

iEEG electrode reconstruction pipeline

interactive-cardiac-function-estimator

Module 1 Assignment for BMEN 6003

iso2mesh

Iso2Mesh - a 3D surface and volumetric mesh generator for MATLAB/Octave

kilosort

Fast spike sorting with drift correction for up to a thousand channels

leaddbs

Lead-DBS is a scientific toolbox facilitating deep brain stimulation electrode locations and connectomic imaging.

legui

Fast, easy-to-use intracranial electrode localization software built entirely in MATLAB

mat_py_mat

Examples and tooling for using spectral parameterization within a Matlab workflow.

mousecam

A head-mounted camera system integrates detailed behavioral monitoring with multichannel electrophysiology in freely moving mice

neuropixel-utils

Utilities for managing Neuropixel datasets and Kilosort results

neuropixels_trajectory_explorer

Neuropixels trajectory explorer with the Allen CCF mouse atlas

nifti_toolbox

MATLAB nifti toolbox (orig. from https://www.mathworks.com/matlabcentral/fileexchange/8797-tools-for-nifti-and-analyze-image) with a couple wrappers

phy

phy: interactive visualization and manual spike sorting of large-scale ephys data

pynapple

PYthon Neural Analysis Package :pineapple:

ref_snake

Snakemake workflow to automatically build and organize reference genomes for common alignment tasks

roast

A simulator for TES

ross

Robust Offline Spike Sorter

spacexr

Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial transcriptomics

spikes

cortex lab code for electrophysiology

spm12

Public Releases of SPM12 - see https://github.com/spm/spm for the Development Version