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http://www.genenetwork.org/

Web platform that provides access to data and tools to study complex networks of genes, molecules, and higher order gene function and phenotypes. Sequence data (SNPs) and transcriptome data sets (expression genetic or eQTL data sets). Quantitative trait locus (QTL) mapping module that is built into GN is optimized for fast on-line analysis of traits that are controlled by combinations of gene variants and environmental factors. Used to study humans, mice (BXD, AXB, LXS, etc.), rats (HXB), Drosophila, and plant species (barley and Arabidopsis). Users are welcome to enter their own private data.

Proper citation: GeneNetwork (RRID:SCR_002388) Copy   

•   Source: SciCrunch Registry
  

http://www.clsi.org/

A not-for-profit membership organization that brings together the global laboratory community to foster excellence in laboratory medicine by facilitating the development of clinical laboratory testing standards based on input from and consensus among industry, government, and health care professionals. CLSI is setting the standard for quality in clinical laboratory testing around the world.

Proper citation: Clinical and Laboratory Standards Institute (RRID:SCR_002382) Copy   

•   Source: SciCrunch Registry
  

http://anatomy.uams.edu/anatomyhtml/neuro_atlas.html

Online educational resource for human brain and spinal cord anatomy through images. Each image is annotated with major structures and coarse dissections.

Proper citation: Neuroscience Course - Atlas Images (RRID:SCR_002381) Copy   

•   Source: SciCrunch Registry
  

http://www.nitrc.org/projects/nptk/

Non-rigid registration / distortion correction tools for enhanced functional localization through the registration of EPI fMRI to high-resolution anatomical MRI.

Proper citation: NPTK (RRID:SCR_002496) Copy   

•   Source: SciCrunch Registry
  

http://www.nitrc.org/projects/nitrc_es/

Support and community integration for the enhanced NITRC services of the Image Repository (IR) and the Computational Environment (CE). The NITRC Computational Environment, an on-demand, cloud based computational virtual machine pre-installed with popular NITRC neuroimaging tools built using NeuroDebian. NITRC Image Repository is built upon XNAT and supports both NIfTI and DICOM images. The NITRC-IR offers 3,733 Subjects, and 3,743 Imaging Sessions searchable across seven projects to promote re-use and integration of valuable NIH-funded data.

Proper citation: NITRC Enhanced Services (RRID:SCR_002494) Copy   

•   Source: SciCrunch Registry
  

http://128.32.118.212/thorfinn/realSFS/

Software program used to estimate allele frequency and SNP calling., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: realSFS (RRID:SCR_002493) Copy   

•   Source: SciCrunch Registry
  

http://bioinf.uta.fi/base_root/

IDbases are locus-specific databases for immunodeficiency-causing mutations. Our aim is to establish database for every immunodeficiency or provide links to those maintained elsewhere. IDbases contain in addition to gene mutation, also information about clinical presentation. Information has been collected from literature as well as received directly from researchers. It would be most glad if those analyzing mutations would send their information by using the interactive web submission available in each database. A number of articles have been published related to IDbases. IDbases are curated and distributed with proprietary MUTbase software suite.

Proper citation: IDbases (RRID:SCR_002378) Copy   

•   Source: SciCrunch Registry
  

http://nipy.org/nibabel/

A Python package for reading and writing a variety of medical and neuroimaging file formats. This includes: ANALYZE (plain, SPM99, SPM2), NIfTI1, as well as MINC. NiBabel is the successor of PyNIfTI.

Proper citation: NiBabel (RRID:SCR_002498) Copy   

•   Source: SciCrunch Registry
  

http://www.nitrc.org/projects/niral_utilities/

Open-source utilities that are C++ based command line applications that allow image analysis and processing using ITK or VTK libraries. Specifically the following utilities are contained thus far: * ImageMath - the swiss army knife image modification * ImageStat - compute stats on images * IntensityRescaler - rescale/normalize intensities using a prior brain tissue segmentation * convertITKformats - convert 3D images in all ITK formats (NRRD, NIFTI, GIPL, Meta etc) * DWI_NiftiNrrdConversion - convert DWI and DTI from/to NRRD and NIFTI, works with UNC DTI tools and FSL * CropTools - crops 3D and 4D images * PolydataMerge - Merges VTK polydata files * PolydataTransform - Transforms polydata files * TransformDeformationField - concatenates or average deformation fields (H-fields or displacement fields) * DTIAtlasBuilder - Creates a DTI average from multiple DTI images

Proper citation: NIRAL Utilities (RRID:SCR_002490) Copy   

•   Source: SciCrunch Registry
  

http://www.r-tutor.com/

Couple of introductory tutorials on basic R concepts that provides an introduction to the R programming language, and illustrates its use by solving elementary statistics textbook exercises. Beyond the basics, they also cover topics of GPU computing in R. An R Tutorial eBook is also available.

Proper citation: R Tutorial - An R Introduction to Statistics (RRID:SCR_002394) Copy   

•   Source: SciCrunch Registry
  

http://www.med.unc.edu/bric/ideagroup/free-softwares/hammer

Software for both groupwise registration and longitudinal registration, which are the necessary steps for many brain-related applications. Specifically, groupwise registration is important for unbiased analysis of a large set of MR brain images. Therefore, in this software package, they have included two of their recently-developed groupwise registration algorithms: 1) Improved unbiased groupwise registration guided with the sharp group-mean image, and 2) Hierarchical feature-based groupwise registration with implicit template (Groupwise-HAMMER for short). On the other hand, they also included their recently-developed groupwise longitudinal registration algorithm that aligns not only the longitudinal image sequence for each subject, but also align all longitudinal image sequences of all subjects to the common space simultaneously.

Proper citation: GLIRT (RRID:SCR_002390) Copy   

•   Source: SciCrunch Registry
  

http://pymzml.github.io/

Python module to parse mzML data in Python based on cElementTree. It is an extension to Python that offers (i) an easy access to mass spectrometry (MS) data that allows the rapid development of tools, (ii) a very fast parser for mzML data and (iii) a set of functions to compare or handle spectra., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: pymzML (RRID:SCR_002500) Copy   

•   Source: SciCrunch Registry
  

http://bioweb.ensam.inra.fr/esther

Database and tools for analysis of protein and nucleic acid sequences belonging to superfamily of alpha/beta hydrolases homologous to cholinesterases. Covers multiple species, including human, mouse caenorhabditis and drosophila., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: ESTHER (RRID:SCR_002621) Copy   

•   Source: SciCrunch Registry
  

http://fmri.wfubmc.edu/software/Bpm

Software toolbox that performs SPM analysis with voxel-wise imaging covariates. The BPM toolbox incorporates information obtained from other modalities as regressors in a voxel-wise analysis, thereby permitting investigation of more sophisticated hypotheses. The BPM toolbox has been developed in Matlab with a user-friendly interface for performing analyses, including voxel-wise multimodal correlation, ANCOVA, and multiple regression. It has a high degree of integration with the SPM (statistical parametric mapping) software relying on it for visualization and statistical inference. Furthermore, statistical inference for a correlation field, rather than a widely used T-field, has been implemented in the correlation analysis for more accurate results. Requirements: * SPM2 or SPM5 * MATLAB version 6.5 or higher

Proper citation: WFU Biological Parametric Mapping Toolbox (RRID:SCR_002613) Copy   

•   Source: SciCrunch Registry
  

http://colibread.inria.fr/discosnp/

Software designed for discovering Single Nucleotide Polymorphism (SNP) from raw sets of reads obtained with Next Generation Sequencers (NGS).

Proper citation: discoSnp (RRID:SCR_002612) Copy   

•   Source: SciCrunch Registry
  

http://etherpad.org/

Web application for real-time collaborative editing. It provides customizable options, a documented API and the ability to convert to various data exchange formats.

Proper citation: Etherpad (RRID:SCR_002611) Copy   

•   Source: SciCrunch Registry
  

http://www.auckland.ac.nz/

Public university in New Zealand that offers degrees in areas such as the arts, business, education, medical and health science, and law.

Proper citation: University of Auckland; Auckland; New Zealand (RRID:SCR_002615) Copy   

•   Source: SciCrunch Registry
  

http://www.vaa3d.org

A handy, fast, and versatile 3D/4D/5D Image Visualization & Analysis System for Bioimages & Surface Objects. Vaa3D is a cross-platform (Mac, Linux, and Windows) tool for visualizing large-scale (gigabytes, and 64-bit data) 3D/4D/5D image stacks and various surface data. It is also a container of powerful modules for 3D image analysis (cell segmentation, neuron tracing, brain registration, annotation, quantitative measurement and statistics, etc) and data management. Vaa3D is very easy to be extended via a powerful plugin interface. For example, many ITK tools are being converted to Vaa3D Plugins. Vaa3D-Neuron is built upon Vaa3D to make 3D neuron reconstruction much easier. In a recent Nature Biotechnology paper (2010, 28(4), pp.348-353) about Vaa3D and Vaa3D-Neuron, an order of magnitude of performance improvement (both reconstruction accuracy and speed) was achieved compared to other tools.

Proper citation: Vaa3D (RRID:SCR_002609) Copy   

•   Source: SciCrunch Registry
  

http://www.trianglebiosystems.com/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. A biomedical device company focused on developing and manufacturing neural hardware solutions for application in medical research using animals when bio-monitoring, recording and stimulation functions are needed. * Neural Recording Equipment * Neural Stimulation Equipment * Data Acquisition Hardware and Software

Proper citation: Triangle BioSystems (RRID:SCR_002603) Copy   

•   Source: SciCrunch Registry
  

http://www.tractor-mri.org.uk/

Software application that includes R packages for reading, writing and visualising magnetic resonance images stored in Analyze, NIfTI and DICOM file formats (DICOM support is read only). It also contains functions specifically designed for working with diffusion MRI and tractography, including a standard implementation of the neighbourhood tractography approach to white matter tract segmentation. A shell script is also provided to run experiments with TractoR without interacting with R.

Proper citation: TractoR: Tractography with R (RRID:SCR_002602) Copy   

•   Source: SciCrunch Registry