WebAlign

Online tool for spatial registration of histological section images from rodent brains to reference 3D atlases.

EBRAINS users can create their own workspace for analysing 2D histological section images.In this space, the data can be uploaded and registered to a common reference atlas using the webAlign service. Several other tools are available as well that can be combined in different workflows for further analysis.

Other software

All software

WebWarp

WebWarp is an online tool for nonlinear refinement of spatial registration of histological section images from rodent brains to reference 3D atlases. Webwarp is compatible with registration performed with the WebAlign tool. Different experimental datasets registered to the same reference atlas allows you to spatially integrate, analyse and navigate these datasets within a standardised coordinate system. The output of Webwarp can be used for analysis in the online QUINT workflow.

Brain atlasesData integration

ilastik

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.

Data analysis and visualisationBrain atlases

LocaliZoom

LocaliZoom allows the viewing and exploring of high-resolution images with superimposed atlas overlays, and the extraction of coordinates of annotated points within those images for viewing in 3D brain atlas space. It is well suited for the extraction of a limited number of coordinates, e.g. representing an electrode track or labelling within a small region of interest.