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http://ncmir.ucsd.edu/downloads/manual_align_rts2000.shtm

Software program to adjust the alignment of two adjacent images. Allows to correct for any misalignment that may occur during auto-alignment step. Serves as a bootstrap to get the images in approximately the right place.

Proper citation: Manual Align RTS2000 (RRID:SCR_007107) Copy   

•   Source: SciCrunch Registry

http://www.wholebraincatalog.org/

THIS RESOURCE IS NO LONGER IN SERVICE, documented May 26, 2016. An open source, downloadable, 3d atlas of the mouse brain and its cellular constituents that allows multi-scale data to be visualized in a seamless way, similar to Google earth. Data within the Catalog is marked up with annotations and can link out to additional data sources via a semantic framework. This next generation open environment has been developed to connect members of the neuroscience community to facilitate solutions for today's intractable challenges in brain research through cooperation and crowd sourcing. The client-server platform provides rich 3-D views for researchers to zoom in, out, and around structures deep in a multi-scale spatial framework of the mouse brain. An open-source, 3-D graphics engine used in graphics-intensive computer gaming generates high-resolution visualizations that bring data to life through biological simulations and animations. Within the Catalog, researchers can view and contribute a wide range of data including: * 3D meshes of subcellular scenes or brain region territories * Large 2D image datasets from both electron and light level microscopy * NeuroML and Neurolucida neuronal reconstructions * Protein Database molecular structures Users of the Whole Brain Catalog can: * Fit data of any scale into the international standard atlas coordinate system for spatial brain mapping, the Waxholm Space. * View brain slices, neurons and their animation, neuropil reconstructions, and molecules in appropriate locations * View data up close and at a high resolution * View their own data in the Whole Brain Catalog environment * View data within a semantic environment supported by vocabularies from the Neuroscience Information Framework (NIF) at http://www.neuinfo.org. * Contribute code and connect personal tools to the environment * Make new connections with related research and researchers 5 Easy Ways to Explore: * Explore the datasets across multiple scales. * View data closely at high resolution. * Observe accurately simulated neurons. * Readily search for content. * Contribute your own research.

Proper citation: Whole Brain Catalog (RRID:SCR_007011) Copy   

•   Source: SciCrunch Registry

http://www.birncommunity.org/collaborators/function-birn/

The FBIRN Federated Informatics Research Environment (FIRE) includes tools and methods for multi-site functional neuroimaging. This includes resources for data collection, storage, sharing and management, tracking, and analysis of large fMRI datasets. fBIRN is a national initiative to advance biomedical research through data sharing and online collaboration. BIRN provides data-sharing infrastructure, software tools, strategies and advisory services - all from a single source.

Proper citation: Function BIRN (RRID:SCR_007291) Copy   

•   Source: SciCrunch Registry

http://www.brainvisa.info/

BrainVISA is a modular an customizable software platform built to host heterogeneous tools dedicated to neuroimaging research. Many toolboxes have already been developed for BrainVISA (T1 MRI, sulcal identification and morphometry, cortical surface analysis, diffusion imaging and tractography, fMRI, nuclear imaging, EEG and MEG, TMS, histology and autoradiography, etc.). Anatomist is a software for interactive visualization of multimodal data and for manipulation of structured 3D objects. It allows to build scenes that merge or combine images, meshes, regions of interest, fibers, textures, color palettes, referential changes, etc. A user can interact in 3D and in real time with the objects of an Anatomist scene: change point of view, select objects, add/suppress objects, change colors, draw regions of interests, do manual registration, etc. BrainVISA main features are: * Harmonization of communications between different software. For instance, BrainVISA toolboxes are using home-made software but also third-party software such as FreeSurfer, FSL, SPM, nipy, R-project, Matlab, etc. * Ontology-based data organization allowing database sharing and automation of mass of data analysis. * Fusion and interactive visualization of multimodal data (using Anatomist software). * Automatic generation of graphical user interfaces. * Workflow monitoring and data quality checking. * Full customization possible. * Runs on Linux, Mac and Windows. * Programming Language: C++, Python * Supported Data Format: ANALYZE, DICOM, GIfTI, MINC, NIfTI-1, Other Format

Proper citation: BrainVISA / Anatomist (RRID:SCR_007354) Copy   

•   Source: SciCrunch Registry

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

A software toolbox that provides a method for generating Region of Interest (ROI) masks based on the Talairach Daemon database. The atlases include Brodmann area, Lobar, Hemisphere, Anatomic Label (gyral anatomy), and Tissue type. The atlases have been extended to the vertex in MNI space, and corrected for the precentral gyrus anomaly. Additional atlases (including non-human atlases) can be added without difficulty., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: WFU PickAtlas (RRID:SCR_007378) Copy   

•   Source: SciCrunch Registry

http://mipav.cit.nih.gov

A Java-based application that enables quantitative analysis and visualization of medical images of numerous modalities such as DTI, PET, MRI, CT, or microscopy. Using MIPAV's standard user-interface and analysis tools, researchers at remote sites (via the internet) can easily share research data and analyses, thereby enhancing their ability to research, diagnose, monitor, and treat medical disorders. MIPAV can be run on any Java-enabled platform such as Windows, UNIX, or Macintosh OS X. Functionality includes segmentation, inter- and intra multi-modality registration, surface rendering, volume rendering and reading and writing a large number of biomedical file formats including: DICOM 3.0, Analyze, NIFTI, SPM, MINC, Phillips, GE, Zeiss, Biorad, jpeg, png, tiff, mrc, fits, interfile, and many more.

Proper citation: MIPAV: Medical Image Processing and Visualization (RRID:SCR_007371) Copy   

•   Source: SciCrunch Registry