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2p-pipeline

custom processing pipeline and analysis code for 2p imaging data

acquisition-tools

code for 2p imaging experiments that syncs I/O and hardware triggers to neural data acquisition (pupil tracking camera, stimulus presentation, etc.)

acquisition2p_class

For managing 2P imaging datasets from preprocessing to activity trace extraction

anttweakbar

A fork of Philippe Decaudin's AntTweakBar library, with cmake and brew/OSX support

axidraw

Software for the AxiDraw drawing machine

blender_render_objs

python script to render objs in blender and a python plugin to load objs exported from 3ds

blob_stimuli

Blob stimuli like those used in Zoccolan 2009 PNAS doi:10.1073/pnas.0811583106

ca_source_extraction

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

caiman

Computational toolbox for large scale Calcium Imaging Analysis, including movie handling, motion correction, source extraction, spike deconvolution and result visualization.

camera-capture-thing

connectome-analysis

Scripts to analyse the hemibrain connectome

coxlab_mwclient_plugins

Lab-specific plugins for the MW Client

coxlab_mwcore_plugins

Lab-specific plugins for the core components of the MW Application Suite

datautils

Data processing utilities

deeplabcut

Markerless tracking of user-defined features with deep learning

dissertation-lets-gooo

draft-areal-characterizations

eyetracker

Software for our self-calibrating eye tracker

face-tracking

tools for analyzing behavior data

facemap

matlab/python GUI for unsupervised video analysis of rodent behavior (capable of processing multiple camera views)

fictrac

FicTrac: A webcam-based method for tracking spherical motion and generating fictive animal paths.

flask_filetree

Example flask blueprint using jquery filetree

flycap

flytracker-analysis

Code to analyze CalTech FlyTracker results

head-fixed-behavior

camera data acquisition, I/O syncing, and data transfer

helperfunctions

Common functions that may be used by all other functions in the Harvey Lab code base.

iocontrol

code for controlling IO devices (in prog)

makeapp

Very simple script to make a Mac OS X app from a script

morph-pov

morph POVray stimuli from A to B

motionmapperpy

Modified Python 3.0 implementation of MotionMapper (https://github.com/gordonberman/MotionMapper)