Unified platform · Module architecture

Is there one platform that handles micro-CT, light-sheet, whole-slide imaging, spatial omics, and MRI together?

If you run, support, or evaluate software for a multi-modal preclinical lab, you work across micro-computed tomography (micro-CT), light-sheet fluorescence, serial whole-slide imaging, spatial omics, and sometimes MRI in the same studies. The platform question is whether each modality stays in a separate application with custom scripts connecting them, or one environment can process, reconstruct, and integrate those datasets on institutional infrastructure with licensing that matches how the lab actually works.

What researchers typically do

Most labs assemble a stack of point tools rather than one integrated platform. Micro-CT commonly opens in Amira, Dragonfly, or scanner vendor software. Whole-slide imaging lives in QuPath, HALO, or Aperio viewers. Spatial omics stays in instrument software or open-source tools such as Seurat or Giotto. Cleared-tissue light-sheet often goes to Fiji/ImageJ, Imaris, or Aivia: platforms rooted in confocal and widefield fluorescence that many labs also use for light-sheet, though terabyte cleared-tissue volumes strain workstation memory and batch workflows on those desktop tools. ImageJ and Imaris overlap with other modalities too, usually through plugins or custom pipelines rather than one shared framework. Connecting modalities for correlative studies usually means manual handoffs, ad hoc Python, or study-specific pipelines that are difficult to audit and reproduce. Procurement adds another layer: institutions must vet software as grant-eligible, auditable investments, not ad hoc tool purchases, while clarifying which capabilities sit in a base platform license, which require add-on modules, and whether data and processing stay on-premises.

One platform, four modules, one sample-space framework

The NeuroSimplicity Imaging Suite solves this problem by combining four dedicated modules on one on-premises platform: Anatomic Imaging (micro-CT and MRI), Molecular Imaging (light-sheet fluorescence), Digital Pathology (serial whole-slide reconstruction), and Spatial Omics (spatial transcriptomics, proteomics, and genomics from serial slides). You can license the modules your lab needs: the first module you select is included in the base platform license, and each additional module is an add-on. When you license all modules together, you can process, reconstruct, and integrate volumes in native sample space through one deterministic framework, without moving data between separate applications.

What the platform enables

  • Four modules: Anatomic Imaging, Molecular Imaging, Digital Pathology, Spatial Omics
  • First module included in base license; additional modules as add-ons
  • Shared native sample-space framework when all modules are licensed
  • Deterministic, auditable batch pipelines across cohorts
  • On-premises private cloud, air-gapped ready

More detail

The Imaging Suite includes four modules: Anatomic Imaging (micro-CT and MRI), Molecular Imaging (light-sheet fluorescence), Digital Pathology (serial whole-slide reconstruction), and Spatial Omics. The first module you select is included in the base platform license; each additional module is an add-on.

For how each modality is processed individually, start with the per-modality guides linked in Next steps.

For cross-modal registration in detail, see the multi-modal integration guide. For capability-by-capability comparison against Imaris, ImageJ, and other tools, see the competitive matrix.

Next steps

Micro-CT analysisAnatomic Imaging Module workflows for ex vivo micro-CT processing and quantificationLight-sheet analysisMolecular Imaging Module workflows for cleared-tissue fluorescence volumesSerial whole-slide imagingDigital Pathology Module workflows for serial histology reconstructionSpatial omics reconstructionSpatial Omics Module workflows for serial slide transcriptomics and proteomicsMulti-modal integrationRegister all modalities from the same specimen in native sample spaceConfigure modulesPlan module selection, licensing, and on-premises deploymentCompetitive matrixCapability-by-capability comparison against point tools and vendor software
Unified Platform for Multi-Modal Preclinical Imaging | NeuroSimplicity