Tools

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Images

MRICloud

MRICloud provides high-throughput neuroinformatics for automated brain MRI segmentation and analytical tools for quantification

Image stack upload/download

ndex

ndex allows exchange of large image volumes with NeuroData

Data visualization

ndviz

NeuroDataViz (ndviz) is a web tool for viewing datasets stored using NeuroData Database Store software.

Web frontend for data

ndwebtools

ndwebtools is a web application that provides NeuroData tools for managing and viewing data on NeuroData's spatial database store.

Synapse Detection

SynapseAnalysis

SynapseAnalysis (PSD) is a framework to evaluate synaptic antibodies for fluorescence array tomography (AT)

EM Synapse Detection

VESICLE

Synapse detection from serial electron microscopy data. VESICLE has now been subsumed by VESICLE-CNN-2.

MR graph analysis

ndmg

ndmg combines diffusion and functional MRI data from individuals to estimate connectome reliably and scalably, and compare populations.

Image registration

ndreg

ndreg is a Python package that performs non-linear affine and deformable image registration.

Calcium Spike Sorting

oopsi

oopsi is a tool for performing model-based spike train inference from calcium imaging. OOPSI has now been subsumed by CaImAn.

Graphs

Download

Connectomes (graph database)
Projectomes (human)

Links to download data

Scalable Analytics

FlashGraph

FlashX are big data analytics tools that perform data analytics in the form of graphs and matrices!

Graph Statistics

graphstats

Utilities and algorithms designed for processing and analysis of graphs with specialized graph statistical algorithms

Vectors

Non-parametric hypothesis testing

MGC

Multiscale Graph Correlation (MGC) is a framework for universally consistent testing high-dimensional and non-Euclidean data.

Clustering

knorR

knorR is a highly optimized and fast library for computing k-means in parallel with accelerations for Non-Uniform Memory Access ('NUMA') architectures.

Classification and regression

Randomer Forest

Randomer Forest is an improved random forest algorithm that achieves better accuracy and scaling than previous implementations on a standard suite of >100 benchmark problems.

Scalable machine learning

FlashX

FlashX are big data analytics tools that perform data analytics in the form of graphs and matrices!

Supervised dimensionality reduction

lolR
lolP

Linear Optimal Low-rank (LOL) projection for improved classification performance in high-dimensional classification tasks

Matrix Exploratory Data Analysis

meda
pymeda

meda implements the top 10 analyses/visualizations we recommend for any matrix valued data.

Local

Cloud

Local

Cloud

Local