Discover neurodata/hierarchical 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

C++

xbrain

all things xbrain

MGC: multiscale graph correlation (pronounced "magic")

MGC-paper

MATLAB

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