Spatial Registration



QuickNII - A major challenge in data mapping is the registration and alignment of 2D image sections in a 3D context. QuickNII is a stand-alone software tool for semi-automated affine spatial registration of sectional image data to a 3D reference atlas coordinate framework and can interact with the Allen Institute Common Coordinate Framework. A key feature in the tool is the capability to generate user defined cut planes through the reference atlas by matching the orientation of the cut plane of the sectional image data. The reference atlas is transformed to match anatomical landmarks in the corresponding experimental images. In this way, the spatial relationship between experimental image and atlas is defined, without introducing distortions in the original experimental images. (QuickNII, RRID:SCR_016854)

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Related publication: Puchades MA, Csucs G, Ledergerber D, Leergaard TB, Bjaalie JG. Spatial registration of serial microscopic brain images to three-dimensional reference atlases with the QuickNII tool. PLoS One. 2019 May 29;14(5):e0216796.


J.G. Bjaalie / Neural Systems Lab (, University of Oslo

Human Brain Project (


HistoloZee 2.0 is a software tool for interactively mapping 2D and 3D molecular and anatomical histology into Common Coordinate Frameworks (CCFs). It has simple, interactive registration workflows that connect user images with CCFs. Planned features include:

  • Concurrent rendering of high-resolution histology and 3D images
  • Slicing of images at arbitrary orientations
  • Seamless multi-scale zooming
  • Surface meshes of anatomical structures
  • Interactive affine registration
  • User-guided deformable registration
  • Persistence of projects in human-readable format
  • Loading of common histology and medical image formats

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Related publication: Adler, D. H., Pluta, J., Kadivar, S., Craige, C., Gee, J. C., Avants, B. B., & Yushkevich, P. A. (2013). Histology-derived volumetric annotation of the human hippocampal subfields in postmortem MRI. NeuroImage, 84, 505-23.


Penn Image Computing and Science Lab (PICSL) (, University of Pennsylvania


Cell Locator is a tool for placing tissue samples into annotated 3D coordinate systems. Users can draw polylines onto arbitrarily oriented slices of the 3D space, give them a physical thickness, and save the results to the JSON file.

This tool is intended to be used by members of the BICCN to localize their cells and tissue samples so that data can be described in a consistent spatial framework. The tool currently supports the Allen Common Coordinate Framework v3, and will be extended to support a human reference space soon.

Cell Locator was developed by Kitware, Inc. It currently supports Windows, and will soon have installers for MacOS and Linux. 

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Allen Institute for Brain Science (

Kitware, Inc. (


SMART (semi-manual alignment to reference templates) extends the WholeBrain framework in R for segmenting and registering experimental images to the Allen Mouse Common Coordinate Framework (CCF). SMART streamlines the processing of large volumetric LSFM datasets and solves issues with non-uniform morphing across the anterior-posterior axis with an interactive “choice game.”  It also accounts for duplicate cell counts in adjacent z images and presents new ways to easily parse apart and interactively visualize the final mapped datasets.

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Related preprint: SMART: An open source extension of WholeBrain for iDISCO+ LSFM intact mouse brain registration and segmentation

Behavioral Neuroscience Research Branch, The National Institute on Drug Abuse Intramural Research Program (