WebAlign is one of several tools developed by the Nesys laboratory, University of Oslo and participating to the Human Brain Project (HBP) and EBRAINS with the aim of facilitating brain atlas based analysis and integration of experimental data and knowledge about the rodent brain. WebAlign is a online tool for user guided affine spatial registration (anchoring) of sectional image data, typically high resolution histological images, to a 3D reference atlas space. A key feature of the tool is its ability to generate user defined cut planes through the atlas templates that match the orientation of the cutting plane of the 2D experimental images (atlas maps).
Through the QUINT Online service: https://rodentworkbench.apps.ebrains.eu/
v0.7
https://webalign.readthedocs.io/en/latest/index.html
- Programming: Gergely Csucs
- Conception, design, validation: Gergely Csucs, Maja A Puchades, Sharon C Yates, Jan G Bjaalie.
- Source code: MIT License
WebAlign (RRID:SCR_026758)
- Puchades MA, Yates SC, Csucs G, Carey H, Balkir A, Leergaard TB, Bjaalie JG. Software and pipelines for registration and analyses of rodent brain image data in reference atlas space. Front Neuroinform. 2025 Sep 24;19:1629388. https://doi.org/10.3389/fninf.2025.1629388
WebAlign is developed by the Neural Systems Laboratory at the Institute of Basic Medical Sciences, University of Oslo, Norway. WebAlign was developed with support from the EBRAINS infrastructure, and funding from the European Union’s Horizon Europe Programme for Research Infrastructures Grant Agreement No. 101147319 (EBRAINS 2.0).
Report issues here on github or email: support@ebrains.eu