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http://atsbio.com/

Commercial supplier of antibodies, assay kits, conjugates and various toxins for biomedical research. ATS's product line is designed to assist scientists in the study of system functions, cell functionality, diseases and disorders.

Proper citation: Advanced Targeting Systems (RRID:SCR_002328) Copy   

•   Source: SciCrunch Registry
  

http://www.nitrc.org/projects/multi_t2/

Software tool designed to assist users in the estimation of multiple relaxation components from MRI T2 weighted spin-echo data such as that produced by a Carr-Purcell-Meiboom-Gill (CPMG) sequence. This problem is important to study myelin content in white matter diseases such as multiple sclerosis. Stimulated echoes arising from non-ideal flip angles are accounted for using the Extended Phase Graph (EPG) algorithm. The distribution is modelled as a small number of discrete components and a Bayesian estimation algorithm is provided to determine the weights and locations of the components as well as the actual flip angle. This algorithm outperforms iterative gradient descent based approaches.

Proper citation: Multicomponent T2 estimation with stimulated echo correction (RRID:SCR_002446) Copy   

•   Source: SciCrunch Registry
  

http://www.thermofisher.com/order/catalog/product/4385261

THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 28, 2017.

Software that performs comparative sequencing, also known as direct sequencing, medical sequencing, PCR sequencing and resequencing with DNA sequencing files. The software is designed for reference based and non-reference based analysis such as mutation detection and analysis, SNP discovery and validation and sequence confirmation.

Proper citation: Variant Reporter Software (RRID:SCR_002329) Copy   

•   Source: SciCrunch Registry
  

http://hardinmd.lib.uiowa.edu/index.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 2, 2025. A medical database with lists, or directories, of information in health and medicine and images of medical conditions. Users may search Hardin MD, browse through the Medical picture gallery, and sort search results by disease or alphabetical letter.

Proper citation: Hardin MD (RRID:SCR_002364) Copy   

•   Source: SciCrunch Registry
  

http://www.bic.mni.mcgill.ca/software/N3/

The perl script nu_correct implements a novel approach to correcting for intensity non-uniformity in MR data that achieves high performance without requiring supervision. By making relatively few assumptions about the data, the method can be applied at an early stage in an automated data analysis, before a tissue intensity or geometric model is available. Described as Non-parametric Non-uniform intensity Normalization (N3), the method is independent of pulse sequence and insensitive to pathological data that might otherwise violate model assumptions. To eliminate the dependence of the field estimate on anatomy, an iterative approach is employed to estimate both the multiplicative bias field and the distribution of the true tissue intensities. Preprocessing of MR data using N3 has been shown to substantially improve the accuracy of anatomical analysis techniques such as tissue classification and cortical surface extraction.

Proper citation: MNI N3 (RRID:SCR_002484) Copy   

•   Source: SciCrunch Registry
  

http://neuronetrix.com/

A portable, highly integrated, internet-enabled, hardware / software platform and patient management system, which includes an online Patient Manager module which complies with the HIPAA Final Security Rule, an event-related potential (ERP) Viewer module to view and analyze raw and average ERP waves, and a Protocol Editor module to simplify the choice and administration of selected ERP protocols. It is also easy to train and administer with non-specialized personnel, and is designed to be used in an out-patient setting. COGNISION TM with auditory or visual event-related potential (ERP) technology, provides a direct physiologic measure of patients' cognitive processing (i.e., a cognitive biomarker).

Proper citation: COGNISION (RRID:SCR_002362) Copy   

•   Source: SciCrunch Registry
  

http://people.csail.mit.edu/msabuncu/sw/RVoxM/

A Bayesian image-based prediction algorithm that is based on the Relevance Vector Machine and Automatic Relevance Detection frameworks, which are popular approaches in Machine Learning. RVoxM adapts this framework to handle images and explicitly models the spatial smoothness in images. RVoxM can be used to learn to predict a binary or continuous variable from image data.

Proper citation: Relevance Voxel Machine (RRID:SCR_002361) Copy   

•   Source: SciCrunch Registry
  

http://millette.med.sc.edu/Lab%209%2610/histology_of_nervous_tissue.htm

A website for a neuroscience lab class from the University of South Carolina that contains images of different parts of the nervous system and allows students to identify each part and answer questions about it. You should be able to (a) recognize nervous tissue in routine histological sections; (b) distinguish peripheral nerves from dense CT and smooth muscle; (c) recognize the morphological differences between myelinated and unmyelinated nerves at both the light microscopic and electron microscopic levels; (d) recognize nerve cell bodies and their component parts; (e) identify and differentiate dendrites and axons; (f) understand and identify various types of neuroglia, including Schwann cells; (g) understand and identify the structural relationship of the Schwann cell cytoplasm and plasma membrane enveloping axons; (h) understand the general features of nerve synapses. You should be able to draw nerves, cell bodies, Nodes of Ranvier, synapses etc. as they would appear under both the electron and light microscopes.

Proper citation: Histology of Nervous Tissue Laboratory Course (RRID:SCR_002367) Copy   

•   Source: SciCrunch Registry
  

https://github.com/gbook/nidb

Neuroimaging database designed to allow simple importing, searching, and sharing of imaging data. NIDB also provides automated pipelining with importing of results back into NIDB which can be searched along with imaging meta data.

Proper citation: NIDB - Neuroinformatics Database (RRID:SCR_002488) Copy   

•   Source: SciCrunch Registry
  

http://www.ddbj.nig.ac.jp

Maintains and provides archival, retrieval and analytical resources for biological information. Central DDBJ resource consists of public, open-access nucleotide sequence databases including raw sequence reads, assembly information and functional annotation. Database content is exchanged with EBI and NCBI within the framework of the International Nucleotide Sequence Database Collaboration (INSDC). In 2011, DDBJ launched two new resources: DDBJ Omics Archive and BioProject. DOR is archival database of functional genomics data generated by microarray and highly parallel new generation sequencers. Data are exchanged between the ArrayExpress at EBI and DOR in the common MAGE-TAB format. BioProject provides organizational framework to access metadata about research projects and data from projects that are deposited into different databases.

Proper citation: DNA DataBank of Japan (DDBJ) (RRID:SCR_002359) Copy   

•   Source: SciCrunch Registry
  

http://www.ncbi.nlm.nih.gov/genome

Database that organizes information on genomes including sequences, maps, chromosomes, assemblies, and annotations in six major organism groups: Archaea, Bacteria, Eukaryotes, Viruses, Viroids, and Plasmids. Genomes of over 1,200 organisms can be found in this database, representing both completely sequenced organisms and those for which sequencing is in progress. Users can browse by organism, and view genome maps and protein clusters. Links to other prokaryotic and archaeal genome projects, as well as BLAST tools and access to the rest of the NCBI online resources are available.

Proper citation: NCBI Genome (RRID:SCR_002474) Copy   

•   Source: SciCrunch Registry
  

http://idealab.ucdavis.edu/software/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. A collection of software tools used for processing and organizing MRI data. The Dicom Importer allows you to to view, assemble, and organize dicom files. Subject Library is a filesystem-based search and reporting tool that can be configured to work with many different organization schemes. This package also contains a python library that can be used to write scripts for custom tasks.

Proper citation: Subject Library (RRID:SCR_002595) Copy   

•   Source: SciCrunch Registry
  

https://github.com/seqan/seqan/tree/master/apps/mason2

Collection of software tools for simulating biological sequences, including simulations of genome fragment sampling, random genomic sequences, methylation levels, and NGS reads.

Proper citation: Mason (RRID:SCR_002476) Copy   

•   Source: SciCrunch Registry
  

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

A set of command line tools allowing 2D and 3D image registration, mainly for medical imaging (although also relevant to other image registration problems).

Proper citation: TAPIR (RRID:SCR_002596) Copy   

•   Source: SciCrunch Registry
  

http://www.med.unc.edu/bric/ideagroup/free-softwares/libra-longitudinal-infant-brain-processing-package

A toolbox with graphical user interfaces for processing infant brain MR images. Longitudinal (or single-time-point) multimodality (including T1, T2, and FA) (or single-modality) data can be processed using the toolbox. Main functions of the software (step by step) include image preprocessing, brain extraction, tissue segmentation and brain labeling. Linux operating system (64 bit) is required. A workstation or server with memory >8G is recommended for processing many images simutaneously. The graphical user interfaces and overall framework of the software are implemented in MATLAB. The image processing functions are implemented with the combination of C/C++, MATLAB, Perl and Shell languages. Parallelization technologies are used in the software to speed up image processing.

Proper citation: iBEAT (RRID:SCR_002470) Copy   

•   Source: SciCrunch Registry
  

http://sve.bmap.ucla.edu/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. An automated online framework for performing validation studies of skull-stripping methods. Registered users may download 40 T1 MRI volumes, skull-strip them with the algorithm of their choice, and upload their segmentation results to the SVE website. The server will then compare the 40 skull-stripped results against a set of manually generated brain masks. The server computes a series of measures for the uploaded data, including Jaccard and Dice measures. It also produces images for visualizing the spatial location of the segmentation errors relative to a common space. The results are archived on the server, and the measures are viewable by visitors to the site.

Proper citation: Segmentation Validation Engine (RRID:SCR_002591) Copy   

•   Source: SciCrunch Registry
  

http://brainmeta.com/connectivity_cortical_references_web.php

Bibliography for primate cortical connectivity. The page displays the articles by their year of publication and links to PubMed.

Proper citation: Primate Cortical Connectivity Database (RRID:SCR_002468) Copy   

•   Source: SciCrunch Registry
  

http://www.nitrc.org/plugins/mwiki/index.php/webmscaleapi:MainPage

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 13, 2026. Venue for discussing and defining standard web interfaces for sharing images, annotations, and analyses of multiscale biological images. The goal is to increase interoperability of code to share the burden of infrastructure, increase code reuse, and allow us to spend more time focused on scientific questions. Please visit our Wiki to start participating. Together we can develop a small group of interfaces which are easy to implement, extensible, and cover the major tasks of developing tools for multiscale data on the web.

Proper citation: Web Interfaces for Multiscale Images (RRID:SCR_002589) Copy   

•   Source: SciCrunch Registry
  

http://www.ebi.ac.uk/gwas/

Catalog of published genome-wide association studies. Genome-wide set of genetic variants in different individuals to see if any variant is associated with trait and disease. Database of genome-wide association study (GWAS) publications including only those attempting to assay single nucleotide polymorphisms (SNPs). Publications are organized from most to least recent date of publication. Studies are identified through weekly PubMed literature searches, daily NIH-distributed compilations of news and media reports, and occasional comparisons with an existing database of GWAS literature (HuGE Navigator). Works with HANCESTRO ancestry representation.

Proper citation: GWAS: Catalog of Published Genome-Wide Association Studies (RRID:SCR_012745) Copy   

•   Source: SciCrunch Registry
  

http://www.scienceexchange.com/facilities/lifetein

LifeTein LLC, located in South Plainfield, New Jersey, was founded for its global custom peptide synthesis services, antibody production services and chemical services. LifeTein offers a wide range of custom research services and a staff of scientists with the first-hand campus-core-facility experience necessary to understanding the role of peptide and protein services in large research projects. LifeTein is the only peptide synthesis manufacturer to have developed its own line of PeptideSyn platform for peptide synthesis and AdjuBooster for antibody production.

Proper citation: LifeTein (RRID:SCR_012626) Copy   

•   Source: SciCrunch Registry