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@neurodata

neurodata

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Location 🇺🇸 United States
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hyppo

Python package for multivariate hypothesis testing

neuroparc

Jupyter Notebook

SPORF

This is the implementation of Sparse Projection Oblique Randomer Forest

m2g

NeuroData's MRI to Graphs (m2g) - connectome estimation package and pipeline

ndstore

code for storing neurodata images and image annotations

ProgLearn

NeuroData's package for exploring and using progressive learning algorithms

Jupyter Notebook

marp-poster-template

Template for an academic poster using Marp

mgcpy-old

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

Jupyter Notebook

ndgrutedb

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

brainlit

Method container for computational neuroscience on brains.

graph-stats-book

Jupyter Notebook

ndreg

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

lol

package for dimensionality reduction under supervised data scenarios

ndio

python interface to neurodata code

nd_template

a blank template that can be cloned demonstrating ocp style

lollipop

Linear Optimal Low Rank Projection

df-dn-paper

Conceptual & empirical comparisons between decision forests & deep networks

Jupyter Notebook

ardent

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

neurodata.io

Homepage for NeuroData

uncertainty-forest

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

Jupyter Notebook

checklists

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

r-mgc

R package for MGC code

ndviz

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

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

CloudReg

SDTF

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

Jupyter Notebook

knorR

R bindings for knor

value-of-ood-data

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

Jupyter Notebook

honest-forests

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

hyppo-papers

Jupyter Notebook

ndio-demos

Demo scripts for the ndio python library

Jupyter Notebook

bilateral-connectome

A paper investigating bilateral symmetry of connectome networks.

maggot_models

Modeling Drosophila larval connectomes

Jupyter Notebook

mgc-matlab

a repo containing the code for mgc in matlab

non-parametric-clustering

Jupyter Notebook

dirtysecrets

dirty secrets of data science

kdg

Exploring and using kernel density algorithms

Jupyter Notebook

MCC

Reproducible code for "Multiscale Comparative Connectomics"

Jupyter Notebook

Graph-Explorer

Web-based graph analytics and some visualization

talks

NeuroData Talks

macho

OCP Wrapper for Ilastik

lifelong_learner

A repository to explore lifelong learning algorithms

Jupyter Notebook

sic

Repository for extensible scientific container paper

ndex

Command line tool to exchange volumetric data with NeuroData

vesicle

reference synapse detection from serial electron microscopy data

mrilab

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

Jupyter Notebook

graphbook-code

Simple package storing functions useful in writing the graphstats book.

Jupyter Notebook

slb

pedigo-project-template

Cookiecutter project template

graphstats

A package for graph statistics

treeple

Jupyter Notebook

ndparse

NeuroData Parse

ndpull

Command line tool to get data from NeuroData

partition_decode

Jupyter Notebook

kasthuri2015

Jupyter Notebook

connectocross

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

Jupyter Notebook

might

dos_and_donts

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

Jupyter Notebook

task-similarity

a repo for exploring task-similarity and its utility for downstream inference

Jupyter Notebook

LOL-paper

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

ood-workshop

brainx

Global Brain Workshop 2016 Repository

LLF_tidy_images

Clean image data for use in LifeLong Forests experiments

nd-faq

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

neuropull

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

class_discr

Jupyter Notebook

badea-mouse

U-Rerf

The unsupervised version of Rerf.

ndreg-old

NeuroData's registration library, built in python using ITK

Jupyter Notebook

hcp_connectomes

Jupyter Notebook

packedForest

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

hierarchical

Jupyter Notebook

xbrain

all things xbrain

Jupyter Notebook

MGC-paper

MGC: multiscale graph correlation (pronounced "magic")

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

ndontology

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

sfn2016

jkmeans

an R package for jk-means

synaptome-stats

Synaptome Statistics

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.

Jupyter Notebook

maggot_connectome

Paper on modeling the larval Drosophila connectome

ND-Overleaf-template

Overleaf latex template for NeuroData

graphutils

Alex's utilities for working with ndmg outputs.

s3-batch-lambdas

DataManager

ndwebsite

boss-export

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

Jupyter Notebook

blog.neurodata.io

This is the repo for the neurodata blog

ClaritySpiePhotonicsPaper

CLARITY paper for SPIE photonics conference

covid-19-data.github.io

covid-19-data webpage

improving-latent-distribution-test

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

Jupyter Notebook

notebooks

Place to host notebooks

Jupyter Notebook

subgraphing

Our code and progress for subgraphing.

SIMPLEX

SIMPLEX reports

mri.neurodata.io