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blendervr

Virtual reality running in blender, using single mouse connected via USB using NI VISA driver

bruker_markpoints

bruker_prairielink

Stream data from PrairieView into MATLAB to allow online processing and analysis

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.

cellpose

a generalist algorithm for cellular segmentation

cellposefornaparm

a little utility to generate cellpose rois for use with naparm

constrained-foopsi

Implementation of the constrained deconvolution spike inference algorithm in Matlab

constrained_nmf

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

dftreg

python module for image sequence registration

generatehologramcuda

matlabvr

Pseudo virtual reality running in Matlab, using pyschtoolbox, Matrox TripleHead2Go, and a rotary encoder connected to an NI DAQ card

monpangle

naparm

Control and design of two-photon photostimulation experiments

ntc_cnmf

source separation

packio

Electrophysiology and synchronization with National Instruments cards

paq2py

Read paq file (from PackIO) into python

pybehaviour

Software and hardware for control of operant conditioning behavioural experiments

readyaml

Read YAML files into MATLAB as struct

rotaryencodervi

sima

Python package for analysis of dynamic fluorescence microscopy data

slmdisplay

java display window for presenting diffraction phase masks on spatial light modulator connected via DVI. iterates through random patterns

slmphasemaskmaker

Implements a weighted GS algorithm using Martin Perssons HOTlab DLL

slmphasemaskmaker3d

Generates phase masks for display on an SLM using a weighted GS algorithm

slmphasemaskmaker_lightpipes

Generate SLM phase masks (MATLAB)

slmphasemaskmaker_pythoncuda

Generate SLM phase masks (Python, CUDA)

slmtransformmaker

Calculate the transform required to map 2P imaging space onto SLM space

slmtransformmaker3d

Calculate the transform required to map 2P imaging space onto SLM space

sta

Standalone python module for performing triggered averaging

stamoviemaker

Generate stimulus triggered average movies and images from activity imaging data

suite2p

Tools for processing 2P recordings