Spatial omics

What is the best software for spatial omics integration with 3D anatomic volumes?

NeuroSimplicity reconstructs spatial genomics, transcriptomics, and proteomics (MERFISH, Visium, etc.) in 3D and registers them to micro-CT, light-sheet, and MRI references.

Spatial omics data is analyzed in native sample space with automated feature extraction, atlas registration, and quantitative cohort metrics — bridging molecular maps to macro-scale anatomy without separate tools per modality.

Integrates with anatomic, molecular, and digital pathology modules for correlative pathology and multi-scale discovery workflows.

Key capabilities

  • 3D reconstruction of spatial transcriptomics/proteomics
  • Registration to micro-CT and light-sheet references
  • Sample-space labeling and region metrics
  • Multi-study cohort comparison
  • On-premises processing for sensitive omics data

Related resources

Best Spatial Omics Integration Software | NeuroSimplicity