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http://brain-development.org/

brain-development.org hosts data and resources used in computational analysis of brain development, including MRI data sets of developing human, software tools, atlases, protocols and software. Several different atlas datasets are available including: * Adult * Pediatric * Neonatal (T2 Templates, Probability Maps) * Neonatal (High-definition, T1 and T2 Templates, Probability Maps) * Fetal (High-definition, T2 Templates, Probability Maps) * Atlas software Anatomical segmentation protocols are available, as well as an Image Registration Toolkit.

Proper citation: brain-development.org (RRID:SCR_005838) Copy   

•   Source: SciCrunch Registry

http://brain-development.org/ixi-dataset/

Data set of nearly 600 MR images from normal, healthy subjects, along with demographic characteristics, collected as part of the Information eXtraction from Images (IXI) project available for download. Tar files containing T1, T2, PD, MRA and DTI (15 directions) scans from these subjects are available. The data has been collected at three different hospitals in London: * Hammersmith Hospital using a Philips 3T system * Guy''s Hospital using a Philips 1.5T system * Institute of Psychiatry using a GE 1.5T system

Proper citation: IXI dataset (RRID:SCR_005839) Copy   

•   Source: SciCrunch Registry

http://neuroviisas.med.uni-rostock.de/neuroviisas.html

An open framework for integrative data analysis, visualization and population simulations for the exploration of network dynamics on multiple levels. This generic platform allows the integration of neuroontologies, mapping functions for brain atlas development, and connectivity data administration; all of which are required for the analysis of structurally and neurobiologically realistic simulations of networks. What makes neuroVIISAS unique is the ability to integrate neuroontologies, image stacks, mappings, visualizations, analyzes and simulations to use them for modelling and simulations. Based on the analysis of over 2020 tracing studies, atlas terminologies and registered histological stacks of images, neuroVIISAS permits the definition of neurobiologically realistic networks that are transferred to the simulation engine NEST. The analysis on a local and global level, the visualization of connectivity data and the results of simulations offer new possibilities to study structural and functional relationships of neural networks. neuroVIISAS provide answers to questions like: # How can we assemble data of tracing studies? (Metastudy) # Is it possible to integrate tracing and brainmapping data? (Data Integration) # How does the network of analyzed tracing studies looks like? (Visualization) # Which graph theoretical properties posses such a network? (Analysis) # Can we perform population simulations of a tracing study based network? (Simulation and higher level data integration) neuroVIISAS can be used to organize mapping and connectivity data of central nervous systems of any species. The rat brain project of neuroVIISAS contains 450237 ipsi- and 175654 contralateral connections. A list of evaluated tracing studies are available. PyNEST script generation does work using WINDOWS OS, however, the script must be transferred to a UNIX OS with installed NEST. The results file of the NEST simulation can be visualized and analyzed by neuroVIISAS on a WINDOWS OS.

Proper citation: neuroVIISAS (RRID:SCR_006010) Copy   

•   Source: SciCrunch Registry

http://www.rad.upenn.edu/sbia/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 2, 2023. Software package used to simulate brain images with local growth / atrophy within a prescribed spherical region. Specifically, given an input image and its segmented image, the location of the center of the spherical region, and the radius of that sphere, it simulates new images that have tissue growth or shrinkage within that pre-specified brain region according to given rates (atrophy for rates less than one and growth for rates greater than one). The algorithm uses an iterative procedure that tries to achieve the given level of volumetric change for brain tissues within the region, by seeking a smooth deformation field, whose Jacobian determinants match the prescribed volume change rate within the region. Note that in the current software, the simulation of growth or atrophy for brain tissue requires that the input spherical region has to cover some CSF or background regions.

Proper citation: Atrophy Simulation Package (RRID:SCR_006046) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/toads-cruise/

A collection of software plug-ins developed for the automatic segmentation of magnetic resonance brain images. The tools include multiple published algorithms developed at Johns Hopkins University. The SPECTRE algorithm performs brain extraction. The TOADS algorithm generates a topology-preserving tissue classification into cortical, subcortical, and cerebellar structures. The CRUISE algorithm produces inner, central, and outer cortical surfaces suitable for computing thickness and other geometric measures. Tools are also included for performing gyral labeling, lesion segmentation, thickness computation, surface visualization, and surface file conversion. All tools are released as plug-ins for the MIPAV software package and were developed using the Java Image Science Toolkit (both available at NITRC: http://nitrc.org). They are therefore cross-platform and compatible with a wide variety of file formats.

Proper citation: TOADS-CRUISE Brain Segmentation Tools (RRID:SCR_005977) Copy   

•   Source: SciCrunch Registry

http://riodb.ibase.aist.go.jp/brain/index.php?LANG=ENG

Atlas of magnetic resonance images and histological sections of a Japanese monkey brain, Rhesus monkey and human. The Brain Explorer allows for display, magnification, and comparison these images. Other formats include a collection of .jpg images, Quicktime VR (allow user to zoom in), and EmonV, a voxel viewer for MacOS X.

Proper citation: Brain Atlas Database of Japanese Monkey for WWW (RRID:SCR_006104) Copy   

•   Source: SciCrunch Registry

http://songbirdtranscriptome.net/

Database containing cDNA clone information of the brains of songbirds. These clones are annotated with behavioral information, as well as links to information of homologous genes of other species. The database includes over 91,000 zebra finch brain cDNAs (2009) sequenced by Duke, ESTIMA, and Rockefeller research groups. The project is a collaborative effort of the Jarvis Laboratory of Duke University, Duke Bioinformatics, and The Genomics group of RIKEN, with Erich D. Jarvis as P.I. and Kazuhiro Wada as Co-P.I. Microarrays with the cDNAs in this database are available at Duke http://mgm.duke.edu/genome/dna_micro/core/spotted.htm and through the NIH Neurosciences Microarray Consortium http://arrayconsortium.tgen.org/np2/public/overview.jsp

Proper citation: Songbird Brain Transcriptome Database (RRID:SCR_006182) Copy   

•   Source: SciCrunch Registry

https://www.braintest.org/brain_test/BrainTest

A portal of online studies that encourage community participation to tackle the most challenging problems in neuropsychiatry, including attention-deficit / hyperactivity disorder, schizophrenia, and bipolar disorder. Our approach is to engage the community and try to recruit tens of thousands of people to spend an hour of their time on our site. You folks will provide data in both brain tests and questionnaires, as well as DNA, and in return, we will provide some information about your brain and behavior. You will also be entered to win amazon.com gift cards. While large collaborative efforts were made in genetics in order to discover the secrets of the human genome, there are still many mysteries about the behaviors that are seen in complex neuropsychiatric syndromes and the underlying biology that gives rise to these behaviors. We know that it will require studying tens of thousands of people to begin to answer these questions. Having you, the public, as a research partner is the only way to achieve that kind of investment. This site will try to reach that goal, by combining high-throughput behavioral assessment using questionnaires and game-like cognitive tests. You provide the data and then we will provide information and feedback about why you should help us achieve our goals and how it benefits everyone in the world. We believe that through this online study, we can better understand memory and attention behaviors in the general population and their genetic basis, which will in turn allow us to better characterize how these behaviors go awry in people who suffer from mental illness. In the end, we hope this will provide better, more personalized treatment options, and ultimately prevention of these widespread and extremely debilitating brain diseases. We will use the data we collect to try to identify the genetic basis for memory and impulse control, for example. If we can achieve this goal, maybe we can then do more targeted research to understand how the biology goes awry in people who have problems with cognition, including memory and impulse control, like those diagnosed with ADHD, Schizophrenia, Bipolar Disorder, and Autism Spectrum Disorders. By participating in our research, you can learn about mental illness and health and help researchers tackle these complex problems. We can''t do it without your help.

Proper citation: Brain Test (RRID:SCR_006212) Copy   

•   Source: SciCrunch Registry

http://www.mouseimaging.ca/

A unique resource and comprehensive imaging facility combining the latest state-of-the-art digital medical imaging technologies for the characterization of mouse functional genomics. The goals of the Mouse Imaging Centre are: * To provide a variety of medical imaging technologies adapted to studying genetically modified mice. These technologies include magnetic resonance (MR) imaging, micro computed tomography (micro-CT), ultrasound biomicroscopy (UBM), and optical projection tomography (OPT). * To screen large numbers of mice for models of human diseases. * To image an individual mouse over time to observe development, disease progression and responses to experimental treatment. * To develop an exciting team of investigators with expertise in imaging techniques, computer science, engineering, imaging processing, developmental biology and mouse pathology. * To work by collaboration with researchers throughout the world. When we look for human diseases in the human population, we make extensive use of medical imaging. Therefore, it makes sense to have available the same imaging capabilities as we investigate mice for models of human disease. The Mouse Imaging Centre (MICe) has developed high field magnetic resonance imaging microscopy, ultrasound biomicroscopy, micro computed tomography, and optical techniques. With these imaging tools, MICe is screening randomly mutagenized mice to look for phenotypes that represent human diseases and is taking established human disease models in mice and using imaging to follow the progression of disease and response to treatment over time. It is clear that imaging has a major contribution to make to phenotyping genetic variants and to characterizing mouse models. MICe is staffed by an exciting new team of about 30 investigators with expertise in imaging techniques, computer science, engineering, imaging processing, developmental biology and mouse pathology. The Mouse Imaging Centre (MICe) is not a fee-for-service facility but works through collaborations. Services include: * Projects involving MicroCT are available as a fee for service. * We will eventually move to the same model above with MRI. * Ultrasound Biomicroscopy is used for cardiac, embryo and cancer studies and is available as fee for service at $100 per study or in some cases on a collaborative basis. * Optical Projection Tomography has only limited availability on a collaborative basis. Mouse Atlas As our images are inherently three-dimensional, we will be able to make quantitative measures of size and volume. With this in mind, we are developing a mouse atlas showing the normal deviation of organ sizes. This atlas is an important resource for biologists as it has the potential to eliminate the need to sacrifice as many controls when making comparisons with mutants. Mouse Atlas Examples: * Variational Mouse Brain Atlas * Cerebral Vascular Atlas of the CBA Mouse * Neuroanatomy Atlas of the C57Bl/6j Mouse * Vascular Atlas of the Developing Mouse Embryo * Micro-CT E15.5 Mouse Embryo Atlas

Proper citation: MICe - Mouse Imaging Centre (RRID:SCR_006145) Copy   

•   Source: SciCrunch Registry

https://www.mbfbioscience.com/brainmaker

Software tool to automatically align sections to visualize brains in 3D. Assists with cell mapping, cytoarchitectonics and other areas requiring characterization of neuronal circuitry to create comprehensive anatomical reference. Automatically creates full resolution, 3D reconstructions of entire brain or any organ from serial sections of whole slide images. Allows to view cells, structures, and lesions, locate neurons expressing particular gene or visualize axonal projections of specific neurons with full anatomical context.

Proper citation: BrainMaker (RRID:SCR_017666) Copy   

•   Source: SciCrunch Registry

https://github.com/AllenInstitute/AllenSDK

Software tool as code for processing and analyzing data in Allen Brain Atlas. Source code for reading and processing Allen Brain Atlas data. Allen SDK focuses on Allen Brain Observatory, Cell Types Database, and Mouse Brain Connectivity Atlas.

Proper citation: Allen Software Development Kit (RRID:SCR_018183) Copy   

•   Source: SciCrunch Registry

https://www.janelia.org/project-team/mouselight

Software imaging platform to generate datasets of whole mouse brains imaged at submicron resolution that allow reconstructions of complete axonal arbors of individual neurons across the entire mouse brain.

Proper citation: MouseLight Project (RRID:SCR_016668) Copy   

•   Source: SciCrunch Registry

https://github.com/vaklip/rsfmri_fconn

Software program for preprocessing resting state functional magnetic resonance imaging (rsfMRI) measurements and calculating region of interest based whole brain functional connectivity.

Proper citation: rsfMRI_fconn calculation (RRID:SCR_016591) Copy   

•   Source: SciCrunch Registry

https://github.com/afids

Open framework for evaluating correspondence between brain images and teaching neuroanatomy.

Proper citation: AFIDs (RRID:SCR_016623) Copy   

•   Source: SciCrunch Registry

http://portal.brain-map.org/

Portal provides access to data and web based applications created for benefit of global research community by Allen Institute for Brain Science. Projects to ombine genomics with neuroanatomy by creating gene expression maps for mouse and human brain. Mouse Brain Atlas, Human Brain Atlas, Developing Mouse Brain Atlas, Developing Human Brain Atlas, Mouse Connectivity Atlas, Non-Human Primate Atlas, and Mouse Spinal Cord Atlas and three related projects Glioblastoma, Mouse Diversity, and Sleep data banks, are used to advance various fields of science especially in neurobiological diseases.

Proper citation: Allen Brain Atlas (RRID:SCR_017001) Copy   

•   Source: SciCrunch Registry

https://kinarm.com/solutions/kinarm-end-point-lab/

Robotics research tool designed to make quantitative neurological assessments of sensorimotor, proprioception, and cognitive brain function by BKIN Technologies. Robotic manipulandum with display for studying arm movements. Allows to assess coordination of limbs at multiple joints while measuring joint specific force.

Proper citation: Kinarm: End-Point Lab (RRID:SCR_017060) Copy   

•   Source: SciCrunch Registry

http://dabi.loni.usc.edu/

Organize, Store, Disseminate, Analyze and Visualize Invasive Neurophysiology Data. Shared archive and resource for human invasive neurophysiology data that have been established by Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative along with software tools for data uploading, visualization and analysis. Users can view and query datasets through online interface but cannot access raw data. Platform utilizes centralized and federated model. Investigators may upload data to central archive or house it themselves.

Proper citation: Data Archive BRAIN Initiative (RRID:SCR_017114) Copy   

•   Source: SciCrunch Registry

https://github.com/Neural-Systems-at-UIO/MeshView-for-Brain-Atlases

Web application for real time 3D display of surface mesh data representing structural parcellations and generation of user defined cut planes from volumetric atlases.

Proper citation: MeshView (RRID:SCR_017222) Copy   

•   Source: SciCrunch Registry

https://www.ncbi.nlm.nih.gov/pubmed/28653482

Software tool to facilitate tractography based deep brain stimulation (DBS) electrode targeting within patient specific stereotactic coordinate system used in operating room.

Proper citation: StimVision (RRID:SCR_017457) Copy   

•   Source: SciCrunch Registry

https://sites.google.com/site/tdtdecodingtoolbox/

Software Matlab toolbox for multivariate analysis of functional and structural MRI data. Software package for multivariate analyses of functional imaging data.

Proper citation: The Decoding Toolbox (RRID:SCR_017424) Copy   

•   Source: SciCrunch Registry