Browsing by Author "Cali, Corrado"

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    Barrio: Customizable Spatial Neighborhood Analysis and Comparison for Nanoscale Brain Structures
    (The Eurographics Association and John Wiley & Sons Ltd., 2022) Troidl, Jakob; Cali, Corrado; Gröller, Eduard; Pfister, Hanspeter; Hadwiger, Markus; Beyer, Johanna; Borgo, Rita; Marai, G. Elisabeta; Schreck, Tobias
    High-resolution electron microscopy imaging allows neuroscientists to reconstruct not just entire cells but individual cell substructures (i.e., cell organelles) as well. Based on these data, scientists hope to get a better understanding of brain function and development through detailed analysis of local organelle neighborhoods. In-depth analyses require efficient and scalable comparison of a varying number of cell organelles, ranging from two to hundreds of local spatial neighborhoods. Scientists need to be able to analyze the 3D morphologies of organelles, their spatial distributions and distances, and their spatial correlations. We have designed Barrio as a configurable framework that scientists can adjust to their preferred workflow, visualizations, and supported user interactions for their specific tasks and domain questions. Furthermore, Barrio provides a scalable comparative visualization approach for spatial neighborhoods that automatically adjusts visualizations based on the number of structures to be compared. Barrio supports small multiples of spatial 3D views as well as abstract quantitative views, and arranges them in linked and juxtaposed views. To adapt to new domain-specific analysis scenarios, we allow the definition of individualized visualizations and their parameters for each analysis session. We present an in-depth case study for mitochondria analysis in neuronal tissue and demonstrate the usefulness of Barrio in a qualitative user study with neuroscientists.
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    NeuroShape: exploiting neural architectures for shape analysis of ultrastructural 3D neuroscience morphologies
    (The Eurographics Association, 2025) Shaffique, Humaira; Shah, Uzair; Alzubaidi, Mahmood; Schneider, Jens; Magistretti, Pierre Julius; Cali, Corrado; Househ, Mowafa; Agus, Marco; Comino Trinidad, Marc; Mancinelli, Claudio; Maggioli, Filippo; Romanengo, Chiara; Cabiddu, Daniela; Giorgi, Daniela
    Recent advances in volume electron microscopy (EM) enable nanometric-scale 3D reconstructions of neural tissue, providing unprecedented opportunities for studying cellular and subcellular morphology in neuroscience. The geometry of structures such as nuclei, neurites, and organelles can encode phenotypic information relevant to both functional specialization and pathological conditions, and thus represents a valuable complement to connectivity-based approaches in connectomics. While previous studies relied on handcrafted descriptors and classical machine learning for morphology analysis, recent progress in deep learning for 3D shape understanding offers new opportunities to learn robust, task-specific representations directly from geometric data. In this work we present NeuroShape, a first exploration of modern deep learning methods for shape analysis of ultrastructural 3D neuroscience morphologies. We introduce two annotated datasets derived from EM reconstructions: one of nuclei envelopes, and one of neurites and neural organelles. We benchmark two state-of-the-art neural architectures for 3D geometry (DiffusionNet [SACO22] and Laplacian2Mesh [DWL∗24]) and compare them against traditional feature-based descriptors previously used in neural morphology analysis. Our preliminary results highlight both the feasibility and the challenges of applying deep learning shape analysis techniques in this domain, and we release the datasets as a reference resource for future studies.