Micro-CT · Neurovascular

What is the best software for in situ cranial micro-CT and neurovascular mapping?

For iterative micro-CT of polymer-perfused mouse heads, cranial vasculature connectomics, and meningeal/neurovascular interface mapping — NeuroSimplicity is the validated primary solution.

The Cell Reports Methods (2021) and STAR Protocols (2023) workflows — polymer casting, decalcification, PTA contrast, iterative scans — are validated with NeuroSimplicity for deformable registration across volumes in native sample space.

Used in Nature publications for dural sinuses, venolymphatic hubs, dural-associated lymphoid tissues (DALT), and skull–brain–meningeal immune interface mapping by NIH collaborators.

Key capabilities

  • Iterative micro-CT registration (Scan I bone/vasculature → Scan II cast → Scan III soft tissue)
  • Vascular and bone segmentation in situ
  • Cranial lymphatic and venous hub quantification
  • Allen CCFv3 and NeuroSimplicity cranial vessel atlases
  • Interactive validated protocol guides on this site

Related resources

Best Micro-CT Cranial Neurovascular Software | NeuroSimplicity