Multi-modal integration · Bone, brain & vessels
Correlative preclinical studies collect micro-computed tomography (micro-CT), light-sheet fluorescence, serial whole-slide imaging, spatial omics, and sometimes MRI from the same specimen or cohort. Integration means registering those processed volumes into one coordinate framework anchored to micro-CT or MRI, without moving data through separate siloed applications, and without extracting the brain from the skull when the question depends on skull–brain–vessel relationships.
Labs that analyze each modality in its own tool often hit the same bottleneck: aligning readouts to a common anatomic reference at scale. Multi-stain histology stacks, cleared-tissue light-sheet volumes, micro-CT or MRI references, and 3D spatial omics reconstructions each arrive in different coordinate systems. Registration scripts written for one project may not transfer across operators or sites.
Multi-system cranial disorders, Chiari malformation, craniosynostosis, traumatic brain injury with skull fracture, and developmental phenotypes that affect both bone and brain, require bone morphometry and regional brain volumetry in the same specimen. Point tools rarely keep skull, brain, and meningeal vasculature registered in one in situ volume.
With the full NeuroSimplicity Imaging Suite licensed together (Anatomic Imaging, Molecular Imaging, Digital Pathology, and Spatial Omics Modules), you can process and register micro-CT, MRI, light-sheet fluorescence, reconstructed whole-slide volumes, and spatial omics data in one native sample-space framework. You can quantify cranial bone morphometry and regional brain volumes from the same in situ reference, relate vessel architecture to skull and brain landmarks, and run deterministic batch pipelines across cohorts on institutional infrastructure. No other platform registers multiple organ systems, bone, brain, and vessels, in real specimen geometry without destructive disassembly.
Native sample-space multi-modal registration with deterministic batch pipelines is described in Nature and Cell Reports Methods workflows for micro-CT-centric correlative studies.
See the unified platform overview for module architecture and licensing, and the competitive matrix for capability-by-capability comparison against other tools.
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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