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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://www.ncdc.noaa.gov/paleo/softlib/paleovu.html

A complete browse and visualization tool for all types of paleoclimate and paleoecological data (Version 1.0 for Windows 3.1 and the Macintosh). Point and click to create queries, list site information, display or plot variables and data, or export the data for further processing and analysis. Note: PaleoVu is no longer maintained or supported. Data content is not being updated, and compatibility problems may exist with newer operating systems. PaleoVu is still suitable as a teaching tool, but our internet-based browsing tools are the most up to date source for paleoclimatic data.

Proper citation: PaleoVu (RRID:SCR_002411) Copy   

•   Source: SciCrunch Registry

http://mgui.wikidot.com

An open source Java-based project intended to provide a graphic user interface (GUI) for interactions between scientists (or enthusiasts) and their data. In its current (beta) form, mgui offers the following functionality: * Cross-platform functionality (with a Java Runtime installation, runs on Linux, Windows, Mac, or Solaris) * 2D rendering of data based upon Java2D, and 3D rendering based upon Java3D * The ability to organize complex datasets into intuitive mgui projects * A processing pipeline interface which allows users to process their datasets with any available Java or native software tools * An extensible I/O framework accommodating a variety of standard and non-standard file formats * Database connectivity using JDBC * Graph visualization based upon the JUNG library * An intuitive Swing-based GUI for managing, querying, and visualizing data * Various CAD-type tools for editing and creating geometry * A computational modelling framework

Proper citation: ModelGUI (RRID:SCR_002441) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/flowBeads.html

Software package for the analysis of flow cytometry bead data. It extends flowCore to provide functionality specific to bead data. One of the goals of this package is to automate analysis of bead data for the purpose of normalization.

Proper citation: flowBeads (RRID:SCR_002440) Copy   

•   Source: SciCrunch Registry

http://air.bmap.ucla.edu/MultiTracer2/MultiTracer.html

A Java application that allows images to be displayed in three dimensions. The tool allows anatomic structures to be traced and the tracings to be saved in a format that facilitates review and revision. It supports NIfTI-1.1 format float, double and signed and unsigned byte, short, and integer formats and provides legacy support for Analyze 7.5 8 and 16 bit images. It provides image display, editing, delineation of structure boundaries, export of traced contours and generation of masked volumes. Images are displayed in 3 orthogonal views. Time series can be displayed as averaged or contrast images and time courses can be visualized graphically. Version 2 provides enhancements to the original MultiTracer feature set.

Proper citation: MultiTracer (RRID:SCR_002445) Copy   

•   Source: SciCrunch Registry

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

Scan-rescan imaging sessions on 21 healthy volunteers (no history of neurological disease) intended to be a resource for statisticians and imaging scientists to be able to quantify the reproducibility of their imaging methods using data available from a generic 1 hour session at 3T. Imaging modalities include MPRAGE, FLAIR, DTI, resting state fMRI, B0 and B1 field maps, ASL, VASO, quantitative T1 mapping, quantitative T2 mapping, and magnetization transfer imaging. All data have been converted to NIFTI format. Please cite: Bennett. A. Landman, Alan J. Huang, Aliya Gifford, Deepti S. Vikram, Issel Anne L. Lim, Jonathan A.D. Farrell, John A. Bogovic, Jun Hua, Min Chen, Samson Jarso, Seth A. Smith, Suresh Joel, Susumu Mori, James J. Pekar, Peter B. Barker, Jerry L. Prince, and Peter C.M. van Zijl. ?Multi-Parametric Neuroimaging Reproducibility: A 3T Resource Study?, NeuroImage. (2010) NIHMS/PMC:252138 doi:10.1016/j.neuroimage.2010.11.047

Proper citation: Multi-Modal MRI Reproducibility Resource (RRID:SCR_002442) Copy   

•   Source: SciCrunch Registry

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

Software package that is a powerful graphical interface that displays, segments, aligns, manipulates, and blends image (pixel) and geometry (real-world coordinates) data simultaneously. Several applications are directly built into MIVA. Registration modes include interactive affine transformations. Fiducial registration tools facilitate rapid alignments for inter-modality volumes. Interactive Region of Interst (ROI) and Volume-of-Interest (VOI) tools exist to segment medical images. Virtually unique to MIVA are its 3D geometry tools and their compatibility with pixel based medical images. A full 3D interactive rat brain atlas is in an fMRI module which walks one through the necessary steps of fMRI. A multiple material surface routine takes segmented medical slices and creates 3D triangulated surfaces that align along all region boarders without overlap or gaps. These surfaces are the direct input into the MIVA tetrahedral mesh generator.

Proper citation: Medical Image Visualization and Analysis (RRID:SCR_002315) Copy   

•   Source: SciCrunch Registry

http://cogprints.org/

An electronic archive for self-archive papers in any area of Psychology, neuroscience, and Linguistics, and many areas of Computer Science, Philosophy, Biology, Medicine, Anthropology, cognitive ethnology, archeology, paleontology, as well as any other portions of the physical, social and mathematical sciences that are pertinent to the study of cognition.

Proper citation: Cogprints: Cognitive Sciences EPrint Archive (RRID:SCR_002314) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/flowCyBar.html

A software package to analyze flow cytometric data using gate information to follow population / community dynamics.

Proper citation: flowCyBar (RRID:SCR_002319) Copy   

•   Source: SciCrunch Registry

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

This simple visualization tool allows to load 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. Very useful for quality control, image comparison.

Proper citation: MriWatcher (RRID:SCR_002318) 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.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