SOFTWARE2017-11-06T12:17:47+00:00

ReproZip

ReproZip allows you to pack your research along with all necessary data files, libraries, environment variables and options.Then anybody can reproduce the research on a different machine, without tracking down and installing the dependencies, or even having to run the same operating system!

More information:  www.reprozip.org
GitHub: github.com/ViDA-NYU/reprozip

Domain Discovery Tool

Domain Discovery Tool (DDT) project. DDT is an interactive system that helps users explore and better understand a domain (or topic) as it is represented on the Web. It achieves this by integrating human insights with machine computation (data mining and machine learning) through visualization. DDT allows a domain expert to visualize and analyze pages returned by a search engine or a crawler, and easily provide feedback about relevance.

GitHub: github.com/ViDA-NYU/domain_discovery_tool

ACHE

ACHE is a focused web crawler. It collects web pages that satisfy some specific criteria, e.g., pages that belong to a given domain or that contain a user-specified pattern. ACHE differs from generic crawlers in sense that it uses page classifiers to distinguish between relevant and irrelevant pages in a given domain. A page classifier can be from a simple regular expression (that matches every page that contains a specific word, for example), to a machine-learning based classification model. ACHE can also automatically learn how to prioritize links in order to efficiently locate relevant content while avoiding the retrieval of irrelevant content.

GitHub: github.com/ViDA-NYU/ache

VisTrails

BirdVis is an interactive visualization system that supports the analysis of spatio-temporal bird distribution models. BirdVis leverages visualization techniques and uses them in a novel way to better assist users in the exploration of interdependencies among model parameters. Furthermore, the system allows for comparative visualization through coordinated views, providing an intuitive interface to identify relevant correlations and patterns.

More information: www.birdvis.org
GitHub: github.com/VisTrails/VisTrails

 

Deformetrica

Deformetrica is a software for the statistical analysis of 2D and 3D shape data. It essentially computes deformations of the 2D or 3D ambient space, which, in turn, warp any object embedded in this space, whether this object is a curve, a surface, a structured or unstructured set of points, or any combination of them.

More information: http://www.deformetrica.org

ITK-SNAP

ITK-SNAP is a software application used to segment structures in 3D medical images. It is the product to create a tool that would be dedicated to a specific function, segmentation, and would be easy to use and learn. ITK-SNAP is free, open-source, and multi-platform.

More information:
http://www.itksnap.org/pmwiki/pmwiki.php
Github: https://github.com/pyushkevich/itksnap

ExoshapeAccel

ExoshapeAccel is a C/C++ application for estimating continuous evolution from a discrete collection of shapes, designed to produce realistic anatomical trajectories.

More information: 
Github:

3D Slicer

3D Slicer is an open source software platform for medical image informatics, image processing, and three-dimensional visualization. Built over two decades through support from the National Institutes of Health and a worldwide developer community, Slicer brings free, powerful cross-platform processing tools to physicians, researchers, and the general public.

More information:https://www.slicer.org
Github: https://github.com/Slicer/Slicer

MriWatcher

MriWatcher is a simple visualization tool allows loading several images at the same time. The cursor across all windows are coupled and you can move/zoom on all the images at the same time. It is very useful for quality control, image comparison.

More information:
https://www.nitrc.org/projects/mriwatcher/
Github: https://github.com/NIRALUser/MriWatcher

DTIPrep

DTIPrep performs a “Study-specific Protocol” based automatic pipeline for DWI/DTI quality control and preparation. This is both a GUI and command line tool. The configurable pipeline includes image/diffusion information check, padding/Cropping of data, slice-wise, interlace-wise and gradient-wise intensity and motion check, head motion and Eddy current artifact correction, and DTI computing.

More information:
https://www.nitrc.org/projects/dtiprep/
Github: https://github.com/NIRALUser/DTIPrep

DTI Atlas Builder

This tool creates an Atlas image as an average of several DTI images that will be registered. The registration will be done in two steps :
– Affine Registration with BRAINSFit
– Non Linear Registration with GreedyAtlas
A final step will apply the transformations to the original DTI images so that the final average can be computed.

More information:
https://www.nitrc.org/projects/dtiatlasbuilder/
Github:
https://github.com/NIRALUser/DTIAtlasBuilder