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3deecelltracker

A python algorithm for tracking cells in 3D time lapse images.

caiman-matlab

Complete Matlab pipeline for large scale calcium imaging data analysis

caimanassist

Helper functions for running caiman's 3D motion correction

calciumvolumetric

python code for analyzing multiplane 2p movies

calsig

Calcium signal processing (quantile matching, normalization, baselining, etc.)

calyxreg

3d image registration for aligning MB calyxes

copytoimageplus

Assuming you have communication between ImageJ and MATLAB via ImageJ-MATLAB, copytoImagePlus allows you to turn a MATLAB array into ImagePlus object.

dblab-schematics

Device and instrument schematics from the de Bivort lab

gitignore

A collection of useful .gitignore templates

imagej_scripts

Scripts for importing ROIs from ca_source_extraction to Fiji for manual refinement

jyang-2

jyang-2.github.io

code documentation

loris

Loris: Database and Analysis application for a Drosophila Lab (or any lab)

mb-odor-rearing

metabolicpathways

Code to examine MetaCyc reaction pathways

ml_toolbox

A Machine learning toolbox containing algorithms for non-linear dimensionality reduction, clustering, classification and regression along with examples and tutorials which accompany the Master level "Advanced Machine Learning" and "Machine Learning Programming" courses taught at EPFL by Prof. Aude Billard

rastermap

A multi-dimensional embedding algorithm

reusedplots

useful plotting functions used across projects

rye2p

Reused code for parsing ThorImage movies and ThorSync recordings (frame times, PID, etc)

ryeutils

useful functions in analysis

sima

Python package for analysis of dynamic fluorescence microscopy data

simpleitk-notebooks

Jupyter notebooks for learning how to use SimpleITK

suite2p

cell detection in calcium imaging recordings

xrsa

`xarray`-based library for working with calcium imaging data and performing representational similarity analysis