Remy Yang's repositories
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
ryeutils
useful functions in analysis
gitignore
A collection of useful .gitignore templates
ImageJ_scripts
Scripts for importing ROIs from ca_source_extraction to Fiji for manual refinement
jyang-2.github.io
code documentation
loris
Loris: Database and Analysis application for a Drosophila Lab (or any lab)
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)
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