QuickNII

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.

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.