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Notebooks and code for the 2023 EMBO course on imaging and data analysis
Behavioral Observation Research Interactive Software
non-parametric inference for convolutional filters in poisson glms
SimBA (Simple Behavioral Analysis), a pipeline and GUI for developing supervised behavioral classifiers
Automated 3D cell detection in very large images
Growthcurver is an R package that fits growth curve data to a standard form of the logistic equation common in ecology and evolution whose parameters (the growth rate, the initial population size, …
Tools for working with CaImAn (Giovannucci et al., 2019, eLife)
Tools to work with Allen Inst CCF data in matlab
Code to call CNMFe through CaImAn or MATLAB
CIAtah (pronounced cheetah): a software package for calcium imaging analysis of one- and two-photon imaging datasets. Documentation: https://git.io/ciatah_docs. Formerly known as calciumImagingAnal…
Computational toolbox for large scale Calcium Imaging Analysis, including movie handling, motion correction, source extraction, spike deconvolution and result visualization.
R package for segmentation, registration and generating web-based brain atlases from microscope images
Official implementation of DeepLabCut: Markerless pose estimation of user-defined features with deep learning for all animals incl. humans
In vivo GCamp behavioral and data processing functions/scripts in MATLAB
Website for Rethomics framework. Hosts tutorial and documentation.
A MINiscope 1-photon-based Calcium Imaging Signal Extraction PIPEline.
A GUI and library for doing multi-fiber photometry
Code for Remedios, Kennedy et al "Social behaviour shapes hypothalamic neural ensemble representations of conspecific sex"
Code repository for analysis routines detailed in the Resendez et al., 2016 Nature Protocols manuscript
Metaboflux allows to predict the flux distribution in a metabolic network. It is based on Petri nets.
Complete Matlab pipeline for large scale calcium imaging data analysis