Using VoluBA, you can upload an image file to a private storage space and register it interactively to the reference space in your web browser. Currently, VoluBA supports the BigBrain model as a reference space. VoluBA is compatible with the EBRAINS 3D Interactive Atlas Viewer, so you directly inspect your aligned data superimposed with brain region maps and other datasets. You can also submit your anchored dataset to EBRAINS curation support for sharing.
Anchoring an image volume to the reference volume in VoluBA consists of 1) uploading data, 2) adjusting coordinate axes orientations and scalings, 3) interactive adjustment of translation and rotation, and 4) optional refinement of the transformation by entering additional corresponding pairs of anatomical landmarks.
Data upload supports NIfTI files, and requires you to authenticate with an ORCID or EBRAINS account to provide a private storage space. All but the data upload steps can be performed and repeated in arbitrary order, and are supported through a history browser which allows to undo actions and roll back to any previous status of alignment. The interface can be switched to either show the two datasets in a superimposed view, or side-by-side, which is usually preferred for entering corresponding landmarks. After performing the anchoring, the aligned data can be directly opened as a semitransparent layer in the EBRAINS Interactive Atlas Viewer to compare it with region maps and image data. The transformation parameters can be downloaded as a json file. Finally, the aligned data can be submitted to EBRAINS curation services to be shared in line with the FAIR guiding principles.
VoluBA
LaunchOnline documentation
Read hereRecorded demo session
Watch hereThe EBRAINS Collaboratory offers researchers and developers a secure environment to work with others. You control the level of collaboration by sharing your projects with specific users, teams or all of the Internet. Many researchers are sharing their work already; several services, tools, datasets, and other resources are publicly available, and many more are available for registered users.
The EBRAINS multilevel human brain atlas provides detailed information on anatomy, connectivity, and function. It links macroanatomical concepts and their intersubject variability with measurements of the microstructural composition and intrinsic variance of brain regions.
Ilastik is a simple, user-friendly tool for interactive image classification, segmentation and analysis. It is built as a modular software framework, which currently has workflows for automated (supervised) pixel- and object-level classification, automated and semi automated object tracking, semi-automated segmentation and object counting without detection. Most analysis operations are performed lazily, which enables targeted interactive processing of data subvolumes, followed by complete volume analysis in offline batch mode. Using it requires no experience in image processing.
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