Micro-CT · Anatomic imaging
Micro-computed tomography (micro-CT) produces three-dimensional anatomic volumes, from ex vivo specimens to iterative in situ cranial scans. You need to process those datasets: run automated feature extraction, visualize structures in 3D, quantify regions, and compare groups across a cohort.
Preclinical labs typically analyze micro-CT in ImageJ/Fiji, Thermo Scientific Amira, Object Research Systems Dragonfly, or instrument vendor viewers. Segmentation and quantification may stay in the same tool or move to custom Python or MATLAB pipelines. Atlas comparison often warps specimens into standard atlas space. Iterative scan registration across contrast stages, terabyte-scale batch processing, and connecting micro-CT to ex vivo light-sheet, serial histology, or whole-slide imaging from the same study usually requires exporting to additional software.
With the NeuroSimplicity Anatomic Imaging Module, you can process micro-CT data on institutional infrastructure in native sample space. You can run automated feature extraction first, then 3D visualization, quantitative analysis, and cohort comparison through deterministic, auditable pipelines. You can register iterative scans and atlases to the sample (Allen Atlas CCFv3, NeuroSimplicity Cranial and Vessel Atlases, and others) so regional metrics reflect true specimen geometry rather than warping into standard space. For the published in situ cranial neurovascular workflow, see the neurovascular imaging guide linked in Next steps.
The Anatomic Imaging Module is one of the modules you select when licensing the Imaging Suite. The first module is included in the base platform license; each additional module is an add-on.
To integrate micro-CT with light-sheet, whole-slide imaging, or spatial omics from the same specimen, see the multi-modal integration guide linked in Next steps.
This workflow is documented in Cell Reports Methods and STAR Protocols, and applied in Nature discovery studies by NIH NINDS collaborators. Full citations, figures, and paper links are on our publications page.
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