Peichao

2pRAM-paper

Notebooks accompanying the 2-photon random access mesoscope (2p-RAM) paper

awesome-computational-neuroscience

A list of schools and researchers in computational neuroscience

awesome-neuroscience

A curated list of awesome neuroscience libraries, software and any content related to the domain.

AztecRetrieval

Bioinformatics repository crawler and updater

bottomupcs

Bottom Up Computer Science

BrainardLabToolbox

Matlab toolbox used on all Brainard Lab machines. May be useful to others.

CaImAn_Matlab

Matlab implementation of a source extraction and spike inference algorithm for large scale calcium imaging data analysis, based on a constrained matrix factorization approach.

CalmAn

Python implementation of a source extraction and spike inference algorithm for large scale calcium imaging data analysis, based on a constrained matrix factorization approach.

COFD_Nature-Commun

Customized code for COFD paper published in Nature Communications

color_vision

color_vision_2p

colortilt

Colortilt psychophysics experiment

computational-neuroscience

Short undergraduate course taught at University of Pennsylvania on computational and theoretical neuroscience. Provides an introduction to programming in MATLAB, single-neuron models, ion channel models, basic neural networks, and neural decoding.

draw.io

Source to www.draw.io

fissa

A Python toolbox for Fast Image Signal Separation Analysis, designed for Calcium Imaging data.

isetbio

Tools for modeling image systems engineering in the human visual system front end

ISI

Code for ISI image acquisition, stimulus presentation, and mouse visual area segmentation.

JRCLUST

JRCLUST

KiloSort

GPU code for spike sorting

micro-manager

Microscope control and image acquisition integrated with ImageJ.

noise_correlation

NoRMCorre

Matlab routines for online non-rigid motion correction of calcium imaging data

OASIS

Deconvolution of calcium imaging data

OASIS_matlab

opticka

Opticka is an object–oriented visual stimulus+experiment manager built on top of the Psychophysics toolbox (PTB) for Matlab. It runs experimental tasks using flexible full state machine logic and easily does dynamic methods-of-constants type experiments with full behavioural control. It uses a class system to create simple to use visual stimuli using experimenter friendly units. Opticka can use an Eyelink eyetracker, Plexon Omniplex neurophysiology data collection and general TTL control using either a cheap LabJack (ms precision) or DataPixx (µs precision). It contains analysis routines linked to Fieldtrip for spike and LFP data easily parsed in terms of the experimental variables.

psychopy

For running psychology and neuroscience experiments

retinotopic_mapping

spike_analysis

spike sorting and analysis

Suite2P

Tools for processing 2P recordings

VolumeRegistration.jl

Subpixel volumetric registration