Ultraliser: a framework for creating multiscale, high-fidelity and geometrically realistic 3D models for in silico neuroscience

Ultraliser is a neuroscience-specific software framework capable of creating accurate and biologically realistic 3D models of complex neuroscientific structures at intracellular (e.g. mitochondria and endoplasmic reticula), cellular (e.g. neurons and glia) and even multicellular scales of resolution (e.g. cerebral vasculature and minicolumns). Resulting models are exported as triangulated surface meshes and annotated volumes for multiple applications in in silico neuroscience, allowing scalable supercomputer simulations that can unravel intricate cellular structure-function relationships. Ultraliser implements a high-performance and unconditionally robust voxelization engine adapted to create optimized watertight surface meshes and annotated voxel grids from arbitrary non-watertight triangular soups, digitized morphological skeletons or binary volumetric masks. The framework represents a major leap forward in simulation-based neuroscience, making it possible to employ high-resolution 3D structural models for quantification of surface areas and volumes, which are of the utmost importance for cellular and system simulations. The power of Ultraliser is demonstrated with several use cases in which hundreds of models are created for potential application in diverse types of simulations. Ultraliser is publicly released under the GNU GPL3 license on GitHub (BlueBrain/Ultraliser).

SIGNIFICANCE

There is crystal clear evidence on the impact of cell shape on its signaling mechanisms. Structural models can therefore be insightful to realize the function; the more realistic the structure can be, the further we get insights into the function. Creating realistic structural models from existing ones is challenging, particularly when needed for detailed subcellular simulations. We present Ultraliser, a neuroscience-dedicated framework capable of building these structural models with realistic and detailed cellular geometries that can be used for simulations.

Anterior Dural Tear in Thoracic and Lumbar Spinal Fractures: Single-Center Experience with Coating Technique and Literature Review of the Available Strategies

Differently from the posterior, the anterior dural tears associated with spinal fractures are rarely reported and debated. We document our experience with a coating technique for repairing ventral dural lacerations, providing an associated literature review on the available strategies to seal off such dural defects. A PubMed search on watertight repair techniques of anterior dural lacerations focused on their association with spinal fractures was performed. Studies on animal or cadaveric models, on cervical spine, or based on seal/gelfoam or “not suturing” strategies were excluded. 10 studies were finally selected and our experience of three patients with thoracic/lumbar spinal fractures with associated ventral dural tear was integrated into the analysis of the surgical techniques. Among the described repair techniques for ventral dural lacerations a preference for primary suturing, mostly trans-dural, was noted (n = 6/10 papers). Other documented strategies were the plugging of the dural opening with a fat graft sutured to its margins, or stitched to the dura adjacent to the defect, and the closure of the dural tear with two patches, both trans-dural and epidural. Our coating techniques of the whole dural sac with the heterologous patch were revealed as safe and effective alternatives strategies, even when patch flaps wrapping nerve roots have to be cut and a fat graft has to be stitched in the patch respectively for sealing off antero-lateral and wide anterior dural tears. Compared to all the documented strategies for obtaining a watertight closure of an anterior dural laceration, the coating techniques revealed advantages of preserving neural structures, being adaptable to anterior and antero-lateral dural tears of any size.

Watertight Robust Osteoconductive Barrier for Complex Skull Base Reconstruction: An Expanded-endoscopic Endonasal Experimental Study

Endoscopic skull base reconstruction (ESBR) following expanded-endoscopic endonasal approaches (EEA) in high-risk non-ideal endoscopic reconstructive candidates remains extremely challenging, and further innovations are still necessary. Here, the aim is to study the reconstructive knowledge gap following expanded-EEA and to introduce the watertight robust osteoconductive (WRO)-barrier as an alternative durable option. Distinctively, we focused on 10 clinical circumstances. A 3D-skull base-water system model was innovated to investigate the ESBR under realistic conditions. A large-irregular defect (31 × 89 mm) extending from the crista galli to the mid-clivus was achieved. Then, WRO-barrier was fashioned and its tolerance was evaluated under stressful settings, including an exceedingly high (55 cmH₂O) pressure, with radiological assessment. Next, the whole WRO-barrier was drilled to examine its practical-safe removal (simulating redo-EEA) and the whole experiment was repeated. Finally, WRO-barrier was kept into place to value its 18-month long-term high-tolerance. Results in all experiments of WRO-barriers were satisfactorily fashioned to conform the geometry of the created defect under realistic circumstances via EEA, tolerated an exceedingly high pressure without evidence of leak even under stressful settings, resisted sudden-elevated pressure, and remained in its position to maintain long-term watertight seal (18 months), efficiently evaluated with neuroimaging and simply removed-and-reconstructed when redo-EEA is needed. In conclusion, WRO-barrier as an osteoconductive watertight robust design for cranial base reconstruction possesses several distinct qualities that might be beneficial for patients with complex skull base tumours.

Lattice cleaving: a multimaterial tetrahedral meshing algorithm with guarantees

We introduce a new algorithm for generating tetrahedral meshes that conform to physical boundaries in volumetric domains consisting of multiple materials. The proposed method allows for an arbitrary number of materials, produces high-quality tetrahedral meshes with upper and lower bounds on dihedral angles, and guarantees geometric fidelity. Moreover, the method is combinatoric so its implementation enables rapid mesh construction. These meshes are structured in a way that also allows grading, to reduce element counts in regions of homogeneity. Additionally, we provide proofs showing that both element quality and geometric fidelity are bounded using this approach.

Lattice Cleaving: Conforming Tetrahedral Meshes of Multimaterial Domains with Bounded Quality

We introduce a new algorithm for generating tetrahedral meshes that conform to physical boundaries in volumetric domains consisting of multiple materials. The proposed method allows for an arbitrary number of materials, produces high-quality tetrahedral meshes with upper and lower bounds on dihedral angles, and guarantees geometric fidelity. Moreover, the method is combinatoric so its implementation enables rapid mesh construction. These meshes are structured in a way that also allows grading, in order to reduce element counts in regions of homogeneity.