QuickNII - Serial section aligner to volumetric atlases

QuickNII is a tool for user guided affine registration (anchoring) of 2D experimental image data, typically high resolution microscopic images, to 3D atlas reference space, facilitating data integration through standardized coordinate systems.

Key features:
- generate user defined cut planes through the atlas templates, matching the orientation of the cut plane of the 2D experimental image data, as a first step towards anchoring of images to the relevant atlas template
- propagate spatial transformations across series of sections following anchoring of selected images

Multi-modality atlasing datasets provided with QuickNII:
- Waxholm Space Atlas of the Sprague Dawley rat brain, version 2 (T2* MRI, DTI, and delineations at 39 μm resolution)
- Allen Mouse Brain Atlas reference atlas, CCFv3 (SST average template, grayscale Nissl volume reconstruction and delineations from 2015 at 25 μm resolution)

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