What is LocaliView?

Localiview is a web application developed by by the NeSys laboratory at University of Oslo with the aim of facilitating brain atlas-based analysis and integration of experimental data and knowledge about the rodent brain. LocaliView is composed of a suite of apps allowing users to register their brain section images to a reference atlas and annotate the registered image sections in order to extract point coordinates of objects of interest like cell somas, aggregated proteins or connection fibers in tract -tracing experiments for example.

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Web applications:

  • CreateZoom for transformation of brain section images to DZI pyramid format allowing annotation of high resolution images

  • WebAlign and WebWarp for registration to a reference atlas in two steps, affine and non-linear

  • LocaliZoom for annotation of the images and creation of point cloud files

  • MeshView for visualisation of the point clouds in the 3D reference atlas

Which atlases are supported?

  1. Allen Mouse Brain Atlas Common Coordinate Framework version 3 (2015 and 2017) (CCFv3) (Wang et al. 2020. Cell, https://doi.org/10.1016/j.cell.2020.04.007. Epub 2020 May 7; RRID:JCR_020999 and RRID:JRC_021000)

  2. Waxholm Atlas of the Sprague Dawley rat, version 4 (WHS rat brain atlas) (Kleven et al. Nat Methods, 2020. https://doi.org/10.1038/s41592-023-02034-3; RRID:SCR_017124)

What is the output of LocaliView?

  • Visualisation of a point cloud file file (JSON format) containing the coordinates of objects segmented out from section images in atlas space and atlas meshes. By using the “screenshot” button, users can obtain a png image file of the main window field of view.

  • The configuration of the current view using the “configuration” button can be exported and reused