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

An efficient level set framework for multi-object segmentation. Its representation inherently prevents overlaps and gaps and it readily preserves object topology and object relationships. MGDM is efficient, storing only a fixed number of functions for any number of objects, and therefore scales well to segmentation problems with many classes and large images. It's representation also avoids some instabilities in other multi-class level set methods. MGDM is cross-platform; MATLAB wrappers, Java source and API are provided, with MIPAV plugins forthcoming.

Proper citation: MGDM: Multi Geometric Deformable Model (RRID:SCR_002311) Copy   

•   Source: SciCrunch Registry

http://olympus.magnet.fsu.edu/galleries/ratbrain/index.html

An image gallery of the rat brain labeled via immunofluorescence in coronal, horizontal, and sagittal thick sections using laser scanning confocal microscopy.

Proper citation: Confocal Microscopy Image Gallery - Rat Brain Tissue Sections (RRID:SCR_002432) Copy   

•   Source: SciCrunch Registry

http://www.ncdc.noaa.gov/paleo/softlib/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 12,2023. A simple, efficient, process-based forward model of tree-ring growth, requires as inputs only latitude and monthly temperature and precipitation.

Proper citation: VS-Lite (RRID:SCR_002431) 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://www.ncdc.noaa.gov/paleo/softlib/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 12,2023. Matlab code for two-factor (location and year) analysis-of-variance model for the calculation of climate anomalies, in which the reference interval is specified as the full length of the dataset. This scheme avoids the affects of shorter (e.g. 1961-1990) reference intervals on the temporal evolution of the spatial standard deviation of climate anomalies. Data files provided.

Proper citation: ANOVA (RRID:SCR_002427) Copy   

•   Source: SciCrunch Registry

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

Training material for the MS lesion segmentation challenge 2008 to compare different algorithms to segment the MS lesions from brain MRI scans. Data used for the workshop is composed of 54 brain MRI images and represents a range of patients and pathology which was acquired from Children's Hospital Boston and University of North Carolian. Data has initially been randomized into three groups: 20 training MRI images, 24 testing images for the qualifying and 8 for the onsite contest at the 2008 workshop. The downloadable online database consists now of the training images (including reference segmentations) and all the 32 combined testing images (without segmentations). The naming has not been changed in comparison to the workshop compeition in order to allow easy comparison between the workshop papers and the online database papers. One dataset has been removed (UNC_test1_Case02) due to considerable motion present only in its T2 image (without motion artifacts in T1 and FLAIR). Such a dataset unfairly penalizes methods that use T2 images versus methods that don't use the T2 image. Currently all cases have been segmented by expert raters at each institution. They have significant intersite variablility in segmentation. MS lesion MRI image data for this competition was acquired seperately by Children's Hospital Boston and University of North Carolina. UNC cases were acquired on Siemens 3T Allegra MRI scanner with slice thickness of 1mm and in-plane resolution of 0.5mm. To ease the segmentation process all data has been rigidly registered to a common reference frame and resliced to isotrophic voxel spacing using b-spline based interpolation. Pre-processed data is stored in NRRD format containing an ASCII readable header and a separate uncompressed raw image data file. This format is ITK compatible. If you want to join the competition, you can download data set from links here, and submit your segmentation results at http://www.ia.unc.edu/MSseg after registering your team. They require team name, password, and email address for future contact. Once experiment is completed, you can submit the segmentation data in a zip file format. Please refer submission page for uploading data format.

Proper citation: MS lesion segmentation challenge 2008 (RRID:SCR_002425) Copy   

•   Source: SciCrunch Registry

http://cibex.nig.ac.jp/data/

Gene expression database system in compliance with MIAME, which is a standard that the MGED Society has developed for comparing and data produced in microarray experiments at different laboratories worldwide. It serves as a public repository for a wide range of high-throughput experimental data in gene expression research, including microarray-based experiments measuring mRNA, serial analysis of gene expression (SAGE tags), and mass spectrometry proteomic data.

Proper citation: CIBEX: Center for Information Biology gene EXpression database (RRID:SCR_002307) Copy   

•   Source: SciCrunch Registry

https://github.com/nh13/DWGSIM

Whole Genome Simulator for Next-Generation Sequencing.

Proper citation: DWGSIM (RRID:SCR_002342) Copy   

•   Source: SciCrunch Registry

http://phil.cdc.gov/phil/home.asp

Database of CDC's pictures organized into hierarchical categories of people, places, and science, presented as single images, image sets, and multimedia files. Much of the information critical to the communication of public health messages is pictorial rather than text-based. Created by a Working Group at the Centers for Disease Control and Prevention (CDC), the PHIL offers an organized, universal electronic gateway to CDC's pictures. Public health professionals, the media, laboratory scientists, educators, students, and the worldwide public are welcome to use this material for reference, teaching, presentation, and public health messages.

Proper citation: Public Health Image Library (RRID:SCR_002463) Copy   

•   Source: SciCrunch Registry

https://github.com/BEETL/BEETL

Software tool that not only compresses FASTQ-formatted DNA reads more compactly than gzip but also permits rapid search for k-mer queries within the archived sequences. The full FASTQ record of each matching read or read pair is returned, allowing the search results to be piped directly to any of the many standard tools that accept FASTQ data as input. Searchable compressed archive for DNA reads.

Proper citation: BEETL-fastq (RRID:SCR_002341) Copy   

•   Source: SciCrunch Registry

https://github.com/BRAINSia/BRAINSTools/tree/master/BRAINSFit

A program for registering images with with mutual information based metric. Several registration options are given for 3,6, 9,12,16 parameter (i.e. translate, rigid, scale, scale/skew, full affine) based constraints for the registration. The program uses the Slicer3 execution model framework to define the command line arguments and can be fully integrated with Slicer3 using the module discovery capabilities of Slicer3

Proper citation: BRAINSFit (RRID:SCR_002340) Copy   

•   Source: SciCrunch Registry

http://www.ncdc.noaa.gov/paleo/softlib/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 12,2023. FORTRAN code for a simple hydrologic-isotopic-balance model for application to paleolake d18O records. Inputs to the model include discharge, on-lake precipitation, evaporation, and the d18O values of these fluid fluxes. Benson and Paillet (2002)

Proper citation: HIBAL (RRID:SCR_002461) Copy   

•   Source: SciCrunch Registry

http://www.arizona.edu/

Public research university in Tucson, Arizona that offers undergraduate and graduate degree programs in psychology, audiology, speech pathology, and medicine.

Proper citation: University of Arizona; Arizona; USA (RRID:SCR_002459) Copy   

•   Source: SciCrunch Registry

http://ftp://ftp.ncbi.nlm.nih.gov/pub/mhc/rbc/Final Archive

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 23, 2019.BGMUT was database that provided publicly accessible platform for DNA sequences and curated set of blood mutation information. Data Archive are available at ftp://ftp.ncbi.nlm.nih.gov/pub/mhc/rbc/Final Archive.

Proper citation: Blood Group Antigen Gene Mutation Database (RRID:SCR_002297) Copy   

•   Source: SciCrunch Registry

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

An advanced viewer for electrophysiological and behavioral data: it can display local field potentials (EEG), neuronal spikes, behavioral events, as well as the position of the animal in the environment. It also features limited editing capabilities.

Proper citation: NeuroScope (RRID:SCR_002455) Copy   

•   Source: SciCrunch Registry

https://github.com/PhKoch/RepARK

Software using a de novo repeat assembly method which avoids potential biases by using abundant k-mers of next-generation sequencing (NGS) whole genome sequencing (WGS) reads without requiring a reference genome.

Proper citation: RepARK (RRID:SCR_002333) Copy   

•   Source: SciCrunch Registry

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