Pinned Repositories
brainwide-behavior-encoding
Some more interactive visualizations of the data reported by Stringer & Pachitariu et al. 2019: Spontaneous behaviors drive multidimensional, brainwide activity.
conv-autoencoder
a convolutional autoencoder in python and keras.
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.
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
student_tix_scanner
keeps you notified about awesome classical student ticket deals in NYC!
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/.
scaling_analysis
Analysis of the dimensionality of neuronal population dynamics as a function of neuron number
SID
Seeded Iterative Demixing (SID) of neuronal activity recordings made using Light Field Microscopy (LFM)
jmmanley's Repositories
jmmanley/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/.
jmmanley/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.
jmmanley/conv-autoencoder
a convolutional autoencoder in python and keras.
jmmanley/PySFM
Some tools for submodular function minimization in Python
jmmanley/two-nn-dimensionality-estimator
Implementation of TWO-NN method for estimating intrinsic dimension (Facco et al., 2017, Scientific Reports).
jmmanley/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.
jmmanley/gazetracker
A :eyes:gaze tracking:eyes: application!
jmmanley/readthedocs-sphinx-multiproject-example
An example of how to use readthedocs with sphinx-multi project
jmmanley/brainwide-behavior-encoding
Some more interactive visualizations of the data reported by Stringer & Pachitariu et al. 2019: Spontaneous behaviors drive multidimensional, brainwide activity.
jmmanley/ClogCatcher
AI for detecting stalled blood vessels in Alzheimer's models
jmmanley/student_tix_scanner
keeps you notified about awesome classical student ticket deals in NYC!
jmmanley/anipose
A framework for scalable markerless 3D tracking
jmmanley/BetaRegression.jl
Regression models for beta distributed responses in Julia
jmmanley/CaImAn
Computational toolbox for large scale Calcium Imaging Analysis, including movie handling, motion correction, source extraction, spike deconvolution and result visualization.
jmmanley/COVID
COVID-19 visualization and analysis
jmmanley/deepinterpolation
jmmanley/DeepLabCut
Markerless tracking of user-defined features with deep learning
jmmanley/facemap
matlab/python GUI for unsupervised video analysis of rodent behavior (capable of processing multiple camera views)
jmmanley/MAxiMuM_processing_tools
Pipeline based on NoRMCorre and CaImAn for segmenting large FOV, volumetric Light Bead Microscopy data.
jmmanley/MotionMapper
Sample implementation of the MotionMapper behavioral analysis algorithms
jmmanley/noisyopt
Python library for optimizing noisy functions.
jmmanley/slurmpy
submit jobs to slurm with quick-and-dirty python
jmmanley/suite2p
cell detection in calcium imaging recordings
jmmanley/VoltageImaging_pipeline
Code sets for processing voltage imaging data
jmmanley/Zebrafish-Tracking
Software for performing offline tracking of zebrafish larvae.