Big mUltimodal hIgh-resolution atLas Data Management

Project aim

The aims of the project are to:

  • Gain deeper insights in the fibre architecture of the brain and its connectivity in regions of clinical interest
  • Develop workflows for integrating high-resolution big data sets into EBRAINS and for registering high-resolution data to the Human Brain Atlas for the use of the scientific community

Project summary

Carl Zeiss Microscopy GmbH is providing a new type of electron microscopes, Multi Beam SEM, mSEM for imaging very large areas of brain tissue at a spatial resolution that is not yet represented in the HBP.

The planned project aims at measuring the same brain slices with 3D-PLI (to visualize fiber architecture at microscopic scales), X-Ray Tomography (to link micro- and nanoscale data), 3D SEM (Scanning Electron Microscopy), mSEM for very large 2D and 3D samples   as well as FIB-SEM (focused ion beam combined with SEM) for nanoscale analysis of fibers, e.g., myelin sheath microstructure. 3D-PLI will be performed at the Forschungszentrum Jülich, X-Ray Tomography at the University of Veterinary Medicine Vienna, 3D SEM at the University of Gothenburg, mSEM at Zeiss Microscopy in Oberkochen and FIB-SEM at the University of Madrid. The data will be spatially anchored and integrated into the Human Brain Atlas. With the planned project, we will also implement workflows to integrate big data into EBRAINS (atlas) and to enable their analysis, as a blueprint for integrating information deriving from several data-intensive imaging modalities.

In a first step, we will perform a proof-of-concept study on mouse tissue with the emphasis on establishing a suitable fixation protocol for post mortem human brain tissue (perfusion fixation typically used for nanostructural analysis is not possible in humans), which is compatible with all applied imaging techniques. A sample processing and data analysis workflow will be established and ultimately applied to tissue from selected human brain regions.

Beyond integrating data into the atlas, the proposed application will facilitate studying brain diseases that affect myelination (e.g., MS) and ease evaluating the success of therapies for neurological disorders such as deep brain stimulation.

Partnering Organisations

Key facts

Time frame: 2020-01-01 - 2023-03-31

Origin: Spontaneous applications

Funding: Helmholtz Association; Carl Zeiss Microscopy GmbH; UPM (Cajal Cortical Circuits Laboratory)