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

  • Efficient and user-friendly tool for image registration
  • Support any section orientation
  • Open source and integrated in analysis pipelines to meet research needs

Software for 2D image registration to 3D 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.

Fine-tune image registration using VisuAlign and the QUINT workflow

VisuAlign is a tool for applying user-guided nonlinear refinements (inplane) to an existing, affine 2D-to-3D registration, such as created using QuickNII. VisuAlign offers an interactive interface that allows users to fine-tune these registrations using more advanced non-linear methods.

Triplet Illus Registration

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.

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.

Other software

All software


Software for 2D image registration to 3D atlas.

Brain atlasesData integration


Nutil aims to simplify the pre-and-post processing of 2D brain section image data from mouse, rat and other small animal models. It can be used to preprocess images in preparation for analysis, and used as part of the QUINT workflow to perform spatial analysis of labelled features relative to a reference brain atlas. Nutil is developed as a stand-alone application with a simple user-interface, requiring little-to-no experience to execute.

Brain atlasesData analysis and visualisation

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