Multi-modal integration · Sample space
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.
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. Connecting everything in one auditable environment remains uncommon outside custom lab pipelines.
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 choose micro-CT or MRI as the anatomic reference for registering the other modalities from the same specimen. You can run deformable registration, atlas registration to the sample, and deterministic batch pipelines across cohorts on institutional infrastructure. Start with the per-modality guides linked in Next steps if you are still building individual processing pipelines.
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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