Pipeline for rodent brain section images annotation and registration to reference 3D atlases.
LocaliView allows users to perform atlas registration of their rodent brain section images and annotate objects for extraction as point clouds visualised in a 3D atlas viewer.
The workflow comprises a suite of tools designed to support atlas-based analyses of series of histological images from mouse or rat brain.
- CreateZoom (transformation of 2D images into pyramid format DZIP)
- WebAlign (Semi-automated Linear Atlas-Registration)
- WebWarp (Nonlinear Refinement of Atlas-Registration)
- LocaliZoom (Serial section image viewer with annotation tool)
- MeshView (3D brain atlas viewerwith solid slicing and point cloud support)
- Programming: Arda Balkir, Gergely Csucs
- Conception, design, validation and documentation: Arda Balkir, Gergely Csucs, Maja A Puchades, Sharon C Yates, Jan G Bjaalie.
- Source code: MIT licence
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
- CreateZoom (RRID:SCR_026625)
- WebAlign (RRID:SCR_026758)
- WebWarp (RRID:SCR_026759 )
- LocaliZoom (RRID:SCR_023481)
- Meshview (RRID:SCR_017222)
LocaliView is developed by the Neural Systems Laboratory at the Institute of Basic Medical Sciences, University of Oslo, Norway. LocaliView 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