SWAN Viewer

Pipeline

SWAN is a transformation pipeline between high-resolution histology, multimodal imaging, patient imaging, and MNI space. We integrate this pipeline for preoperative and postoperative functional neurosurgery research while preserving the scientific distinction between microscopy, blockface imaging, specimen MRI, patient MRI, and standardized space.

Planned capabilities

SwanWarp and SwanViewer are in the final phase of development. The pipeline is designed to include:

• Slice navigation across the histological series
• Modality switching between brightfield histology, darkfield microscopy, blockface imaging, in situ specimen MRI, and MNI-space views
• Overlay controls for registered images and anatomical labels
• Opacity controls for multimodal comparison
• Metadata panels for slice, modality, and registration information
• Quality-control visualization
• Download links for released public resources
• MNI-space label and segmentation previews
• Segmentation of brain structures in high-resolution histology and warping into MNI space and vice versa, including electrodes, lesions, and regions of interest, through a visual-interface pipeline in 3D Slicer.
• Support for educational and research-oriented anatomical exploration

These capabilities are being finalized and should not be interpreted as a fully public data-download interface.

SwanWarp and SwanViewer

SwanWarp is the SWAN registration and warping framework. SwanViewer is the 3D Slicer-based viewer and interaction module for integrating registration, visualization, segmentation, and bidirectional warping between high-resolution histology and MNI or patient imaging spaces.

Current status

SwanWarp and SwanViewer are under final development. We are finalizing the transformation, visualization, and interaction workflow before public release.

Scientific scope

Present a reliable and collaborative bridge between histology, in vivo imaging, and functional neurosurgery.

Integration context

SWAN is being integrated with 3D Slicer through SwanWarp and SwanViewer. SwanWarp provides the registration and warping framework, while SwanViewer provides the visualization and interaction module.

MNPS relates to preoperative stereotactic planning. Lead-DBS relates to postoperative imaging analysis. SWAN can be warped into patient space through MRI–MRI registration, allowing individual atlas registration. These workflows are not presented as clinically validated SWAN tools.