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Toolkit

Neuroimaging

Several Allen Brain Atlas datasets include Magnetic Resonant Imaging (MRI), Diffusion Tensor (DT) and Computed Tomography (CT) scan data that are open and downloadable.  The imaging protocols are customized to the experimental workflow and data type, summarized below.  Full details are included in the technical documentation for each project.   Refer to the Terms of Use for guidelines on citation and use of the data.

Neuroimaging data (MRI, DTI) for adult human brain

Magnetic resonance imaging and diffusion tensor imaging data is available in downloadable TAR Archive files (.tgz)  through the NIH BrainSpan Project, with detailed descriptions of data acquisition in the Technical Whitepapers.  The links below will prompt for file download.

Neuroimaging data for the developing human brain

NIH BrainSpan data is available for three prenatal specimens: 19 pcw (post-conception weeks), 21 pcw, and 22 pcw, from 3T and 7T scans. MR images include T1, T2*, and proton density as well as the set of FLASH acquisitions used to construct these images. Additionally, 3T diffusion data are available for the 21 pcw specimen at 250um and 400um resolutions. BrainSpan technical documents contain detailed methods and scan parameters. Each dataset was post-processed to rotate the brain and skull-strip the images. Data files are in FreeSurfer file formats.

Download indexed files

Neuroimaging data for adult Rhesus macaque brain

MRI data is available as DICOM files from three 48-month Macaca mulatta brain hemispheres through the Supplemental Data portal, as part of the NIH Blueprint NHP project. Refer to the technical documentation for detailed methods and scan parameters.

Neuroimaging data for clinical cases of glioblastoma

The Ivy Glioblastoma Atlas Project included the acquisition of medical imaging data from adult human brain, covering pathological and non-pathological states. MRI and CT data are available; DICOM files from 39 patients can be downloaded through the cancer imaging archive service. Detailed protocols are also available in the publication, "An anatomic transcriptional atlas of human glioblastoma," Science 360, 660-663 (2018). doi:10.1126/science.aaf2666.