What is LocaliZoom?

EBRAINS LocaliZoom serial section image viewer provides an intuitive way of navigating high-resolution 2D image series coupled with segmentation overlay, from a web browser. At its core, it is a web-based pan-and-zoom 2D image viewer coupled with a volumetric atlas slicer, and a navigational aid showing the entire image series as a “filmstrip”. Building on the open standard Deep Zoom Image (DZI) format, it is able to efficiently visualise very large brain images in the gigapixel range, allowing to zoom from common, display-sized overview resolutions down to the microscopic resolution without downloading the underlying very large image dataset.

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In addition, LocaliZoom is available as a web app in the EBRAINS workflow LocaliView. The LocaliView workflow is accessible with an EBRAINS account.

Key features:

  • Visualisation of experimental histological section images with atlas overlay

  • Display of the atlas region name when pointing the mouse at the region of interest

  • Annotations and extraction of coordinate points when enabled

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Dataset DOI: https://doi.org/10.25493/G5VR-63E

Which atlases are supported

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 3 and 4 (WHS rat brain atlas) (Osen et al. 2019. NeuroImage, https:doi.org/10.1016/j.neuroimage.2019.05.016; Kleven et al. Nat Methods, 2020. https://doi.org/10.1038/s41592-023-02034-3; RRID:SCR_017124)

What is the output of LocaliZoom?

-A registration file (lz format) containing the coordinates of your annotated points in atlas space. This file is then used in the workflows automatically.