Serial slides · Spatial omics

How do labs reconstruct and interact with spatial omics data, especially from serial slides?

Spatial omics maps transcriptomic, proteomic, and genomic profiles across tissue, as spot grids, segmented cells, or continuous coordinates. Scientific questions such as vessel paths, immune microenvironments, and tumor infiltration often require serial sections, but aligning those sections or reconstructing in 3D is challenging, particularly without an anatomic reference such as matching whole-slide imaging or micro-CT.

What researchers typically do

Most labs lack a reproducible way to move beyond per-slide 2D viewers supplied by instrument vendors or tools like Seurat, Giotto, or custom Python notebooks. Serial-section spatial experiments require aligning readouts across consecutive slides, similar to histology reconstruction but with high-dimensional feature data at each coordinate. Recent open-source and generative-AI reconstruction tools attempt to infer three-dimensional structure from sparse 2D spatial data, but outputs are typically non-deterministic, difficult to validate against ground-truth anatomy, and disconnected from micro-CT, light-sheet, or whole-slide references collected on the same specimen. Connecting reconstructed omics volumes to those anatomic references in one auditable environment remains uncommon outside custom lab pipelines.

Spatial omics reconstruction you can navigate in 3D

With the NeuroSimplicity Spatial Omics Module, you can reconstruct spatial genomics, transcriptomics, and proteomics data in three dimensions, including serial slide experiments, and explore those volumes interactively on institutional infrastructure. You can align serial-section spatial readouts across the stack through deterministic, auditable pipelines rather than generative inference alone. When you license the Digital Pathology and Anatomic Imaging Modules together with Spatial Omics, you can explore reconstructed omics volumes aligned to histology, in situ micro-CT, and light-sheet data from the same specimen in native sample space.

What the platform enables

  • 3D reconstruction of spatial transcriptomics, genomics, and proteomics
  • Serial slide spatial omics alignment and interactive 3D exploration
  • Automated feature extraction and region metrics in sample space
  • Deterministic, auditable batch processing across cohorts
  • Cross-modal integration when the full Imaging Suite is licensed

More detail

The Spatial Omics 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.

Serial slide spatial omics shares reconstruction logic with serial whole-slide histology. See the digital pathology guide linked in Next steps.

To register spatial omics volumes to micro-CT, light-sheet, or reconstructed histology from the same specimen, see the multi-modal integration guide linked in Next steps.

Next steps

Serial whole-slide imaging guideReconstruct serial histology stacks; shared workflow with serial spatial slidesLight-sheet analysis guideLight-sheet fluorescence volumes that often pair with spatial omics studiesConfigure Spatial Omics ModulePlan module licensing for spatial omics reconstruction throughputMulti-modal integrationRegister spatial omics to micro-CT, light-sheet, and reconstructed histology
Spatial Omics Reconstruction & 3D Interaction | NeuroSimplicity