Scalable Brain Atlas

Recently, we found a very nice and free tool which could be interesting for our Neuroscientist users: the Scalable Brain Atlas (Developed at the Donders Institute, Radboud University and Medical Center Nijmegen).
This website offers:
1) The access to a large collection of more than 20 brain atlases of different species (mouse, rat, human, macaque, etc…), with a display of the different brain regions in 2D or 3D.

2) An online tool called SBA Composer: a 3d viewer in which users can upload their own data and display them together with brain region meshes and reference image sections. So, this tool allows to overlay the atlas of your choice with your 2D or 3D microscopy images, in addition to available 3D reconstructions of a large range of brain regions.

So, you can now think about the possibility to directly put your images from confocal, 2-photon, light-sheet microscopes or Nanozoomer directly on this ready-to-use 3D frame.
It is possible to import different 2D or 3D formats like multiseries tiff but also 3D reconstructions from our 3D analysis sofwares Imaris and Arivis Vision4D.
The result can be exported as snapshots (in PNG, see figure below) or in 3D formats (X3D or VRML formats which can be imported on open-source softwares like MeshLab or Blender).
Scalable Brain Atlas

2D export images from SBA Composer. A) Mouse brain with 80% of transparency ; B) Mouse brain + Ammon’s horn in 3D ; C-D) Mouse brain + image from Nanozoomer + Ammon’s horn in 3D without (C) or with (D) transparency

 

In parallel, the Fiji plugin Allen Brain BIOP Aligner (BioImaging And Optics Platform – BIOP) currently under development, will allow the registration of 2D sections to 3D atlas. For instance, multiresolution images from Nanozoomer will be directly read and export regions in it. Release early 2021.

Interface of the future Fiji plugin Allen Brain BIOP Aligner

 

Don’t hesitate to contact us if you need more information concerning these tools!