Discover neurodata/MGC-paper Open Source project by @neurodata

code for storing neurodata images and image annotations

ndstore

NeuroData's package for exploring and using progressive learning algorithms

ProgLearn

Template for an academic poster using Marp

marp-poster-template

CSS

mgcpy-old

MGCPY WILL NO LONGER BE UPDATED. THE NEW REPO CAN BE FOUND HERE:

Pipeline and tools for estimating human connectomes from Diffusion, Structural, and Functional MRI

ndgrutedb

Method container for computational neuroscience on brains.

brainlit

graph-stats-book

Perform image registration of 2D and 3D volumes using state-of-the-art deformable registration.

ndreg

C++

lol

package for dimensionality reduction under supervised data scenarios

ndio

python interface to neurodata code

a blank template that can be cloned demonstrating ocp style

nd_template

Linear Optimal Low Rank Projection

lollipop

Conceptual & empirical comparisons between decision forests & deep networks

df-dn-paper

Affine and Regularized DEformative Numeric Transform (ardent) is a Python package for performing image registration using LDDMM.

ardent

neurodata.io

Homepage for NeuroData

Conditional probability, conditional entropy, and mutual information estimation in Python. https://arxiv.org/abs/1907.00325

uncertainty-forest

this repo contains a number of checklists that we find very useful

checklists

NeuroDataViz: Web visualization and analysis for neuroimaging datasets. Powered by Neuroglancer.

r-mgc

R package for MGC code

ndviz

JavaScript

nd_ed

Collection of educational resources. Primarily focused on skills that are helpful in the NeuroData lab or the Neuro Data Design course at Johns Hopkins University.

goat

A paper (in progress) on graph matching via optimal transport. On arxiv at https://arxiv.org/abs/2111.05366

Exploring streaming options for decision trees and random forests. Based on scikit-learn fork.

CloudReg

MATLAB

SDTF

The value of out-of-distribution data (ICML 2023)

knorR

R bindings for knor

value-of-ood-data

Honest decision forests and trees implemented efficiently and scikit-learn compliant.

honest-forests

hyppo-papers

Demo scripts for the ndio python library

ndio-demos

A paper investigating bilateral symmetry of connectome networks.

bilateral-connectome

Modeling Drosophila larval connectomes

maggot_models

a repo containing the code for mgc in matlab

mgc-matlab

non-parametric-clustering

Gui's repo

dirty secrets of data science

dirtysecrets

kdg

Exploring and using kernel density algorithms

Reproducible code for "Multiscale Comparative Connectomics"

MCC

Web-based graph analytics and some visualization

Graph-Explorer

talks

NeuroData Talks

macho

OCP Wrapper for Ilastik

A repository to explore lifelong learning algorithms

lifelong_learner

Repository for extensible scientific container paper

sic

Command line tool to exchange volumetric data with NeuroData

ndex

reference synapse detection from serial electron microscopy data

vesicle

MATLAB

mrilab

A repository containing the dockerfile for a docker container running FSL, AFNI, FlashX, ndmg, and fngs on Ubuntu 16.04.

Simple package storing functions useful in writing the graphstats book.

graphbook-code

Cookiecutter project template

slb

pedigo-project-template

A package for graph statistics

graphstats

treeple

ndparse

NeuroData Parse

Command line tool to get data from NeuroData

ndpull

partition_decode

kasthuri2015

Connectocross: statistical characterizations and comparisons of nanoscale connectomes across taxa (A paper in progress)

connectocross

Experiments showing the do's and don'ts of connectome analysis

might

dos_and_donts

code for generating figures in my Low-rank Optimal Linear Discriminant Analysis

LOL-paper

Global Brain Workshop 2016 Repository

ood-workshop

brainx

Clean image data for use in LifeLong Forests experiments

LLF_tidy_images

A collection of frequently asked questions (and answers) for prospective PhD students considering joining NeuroData and/or BME@JHU.

nd-faq

neuropull

A (soon to be) lightweight Python package for accessing single-cell connectome networks with metadata.

class_discr

badea-mouse

The unsupervised version of Rerf.

U-Rerf

ndreg-old

NeuroData's registration library, built in python using ITK

hcp_connectomes

A memory efficient and fast random forest which produces trees with fast prediction speeds.

packedForest

hierarchical

xbrain

bgm

Repository for the paper "Bisected graph matching improves automated pairing of bilaterally homologous neurons from connectomes" https://direct.mit.edu/netn/article/doi/10.1162/netn_a_00287/113527/Bisected-graph-matching-improves-automated-pairing

Manage/query/update a MongoDB that contains the Allen Research Atlas Ontology

ndontology

an R package for jk-means

sfn2016

jkmeans

synaptome-stats

graph-testing

latex-template

futureinstitute

semipar-cci

combining-representations

A repository to implement, deploy and extend the method described in Learning to rank via combining representations.

Paper on modeling the larval Drosophila connectome

maggot_connectome

Overleaf latex template for NeuroData

ND-Overleaf-template

Alex's utilities for working with ndmg outputs.

graphutils

s3-batch-lambdas

DataManager

ndwebsite

boss-export

Export data from BOSS in bulk from w/in BOSS AWS environment

This is the repo for the neurodata blog

blog.neurodata.io

CLARITY paper for SPIE photonics conference

ClaritySpiePhotonicsPaper

Code for Valid Two-Sample Graph Testing via Optimal Transport Procrustes and Multiscale Graph Correlation: Applications in Connectomics

covid-19-data.github.io

covid-19-data webpage

improving-latent-distribution-test

notebooks

Place to host notebooks

Our code and progress for subgraphing.

subgraphing

SIMPLEX

mri.neurodata.io

pcc

On the power of comparative connectomics