Registering different experimental neuroscience datasets to the same reference atlas allows you to spatially integrate, analyse and navigate these datasets within a standardised coordinate system. Moreover, registering these datasets to an atlas allows them to inherit the spatial information associated with a known 3D atlas or map. 2D histological images of rat or mice brains can be quickly and easily spatially registered to 3D reference atlases using QuickNII; furthermore, this registration can be fine-tuned using non-linear adjustments in VisuAlign. Both tools are available as downloadable desktop applications with user-friendly graphical interfaces and tutorials for getting started.

  • Efficient semiautomatic affine registration of serial 2D images to a 3D reference atlas
  • Optimise initial registration using non-linear adjustments
  • Easily customise atlas overlay plates for your serial sections
  • Save the 3D spatial locations of all your sections in atlas space for further spatial analyses


Atlas registration tools

Register mouse and rat 2D brain images to a 3D reference atlas

QuickNII is a stand-alone tool for user-guided affine spatial registration of murine sectional image data to a 3D reference atlas space. While useful for registering single images, it excels at registering a series of images via a user-friendly interactive interface. The reference atlas is transformed to match anatomical landmarks in the corresponding experimental images without introducing transformations in the original images. Following user-defined anchoring of a limited number of sections containing key landmarks, atlas overlay plates for all remaining section images are generated by QuickNII, greatly reducing the number of manual steps required. VisuAlign offers an interactive interface that allows users to fine tune these registrations using more advanced non-linear methods.

Outputs from these tools are customised atlas maps and image coordinates for each section, which enables quantitative spatial and atlas-based analyses, such as the QUINT workflow.

Use cases

Use QuickNII and VisuAlign for

  • Identification of brain regions in histological brain section image series
  • Mapping the position of 3D reconstructed neurons
  • Cell count analysis using the QUINT workflow


Participate in the 2D image registration community


Puchades M.A., Csucs G., Ledergerber D., Leergaard T.B., Bjaalie J.G. (2019) Spatial registration of serial microscopic brain images to three-dimensional reference atlases with the QuickNII tool. PlosOne. 14(5) : e0216796. doi: 10.1371/journal.pone.0216796

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