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anipose

A framework for scalable markerless 3D tracking

betaregression.jl

Regression models for beta distributed responses in Julia

brainwide-behavior-encoding

Some more interactive visualizations of the data reported by Stringer & Pachitariu et al. 2019: Spontaneous behaviors drive multidimensional, brainwide activity.

caiman

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

clogcatcher

AI for detecting stalled blood vessels in Alzheimer's models

conv-autoencoder

a convolutional autoencoder in python and keras.

covid

COVID-19 visualization and analysis

deepinterpolation

deeplabcut

Markerless tracking of user-defined features with deep learning

facemap

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

forms

Flexible Object Reconstruction from Multiple Silhouettes. Cashman & Fitzgibbon, 'What Shape are Dolphins? Building 3D Morphable Models from 2D Images', 2012. Updated 2018, Jason Manley.

gazetracker

A :eyes:gaze tracking:eyes: application!

maximum_processing_tools

Pipeline based on NoRMCorre and CaImAn for segmenting large FOV, volumetric Light Bead Microscopy data.

motionmapper

Sample implementation of the MotionMapper behavioral analysis algorithms

noisyopt

Python library for optimizing noisy functions.

phi_toolbox

Toolbox for practical calculations of integrated information under the gaussian assumption. See their original papers for details: Oizumi et al., 2016, PLoS Computational Biology & Oizumi et al., 2016, PNAS. Obtained from https://figshare.com/articles/phi_toolbox_zip/3203326.

pysfm

Some tools for submodular function minimization in Python

readthedocs-sphinx-multiproject-example

An example of how to use readthedocs with sphinx-multi project

slurmpy

submit jobs to slurm with quick-and-dirty python

student_tix_scanner

keeps you notified about awesome classical student ticket deals in NYC!

suite2p

cell detection in calcium imaging recordings

two-nn-dimensionality-estimator

Implementation of TWO-NN method for estimating intrinsic dimension (Facco et al., 2017, Scientific Reports).

vgg-multiple-view-geometry

A set of MATLAB utilities for multiple view geometry, provided alongside Hartley & Zisserman's "Multiple View Geometry in Computer Vision, Second Edition" (2004). Obtained from http://www.robots.ox.ac.uk/~vgg/hzbook/code/.

voltageimaging_pipeline

Code sets for processing voltage imaging data

zebrafish-tracking

Software for performing offline tracking of zebrafish larvae.