Bioimage analysis pipelines Segmentation, tracking, denoising, classification, and quality control convert microscopy into quantitative biological state variables. 
Research
Research area · Modeling and bioimage analysis
CompBio
This work connects measurement and mechanism: particle models for cell and nuclear mechanics, image-analysis pipelines for multiplexed microscopy, deep-learning tools for fluorescent reporters, and continuum models for cardiac electromechanics.
Our
Unique vision
CompBio joins the lab's computational modeling and bioimage analysis work instead of splitting them into separate cultures. BIO-POINT, SEM2, DeepFUCCI, and the imaging-analysis work with Michele Torre all belong here because they turn experiments into quantitative objects that can be compared, modeled, and explained.
Platforms and capabilities
Images, models, and mechanism
Bioimage analysis pipelines Segmentation, tracking, denoising, classification, and quality control convert microscopy into quantitative biological state variables. Multiscale physiological modeling From molecular dynamics to continuum and isogeometric analysis, the lab picks the model scale that can actually explain the experiment. Related publications
Articles and preprints in this area
Including collaborations; listed newest to oldest.
Peer-reviewed article MicroSplit: semantic unmixing of fluorescent microscopy data Ashesh Ashesh, Federico Carrara, Igor Zubarev, Vera Galinova, Melisande Croft, Melissa Pezzotti, Daozheng Gong, Francesca Casagrande, Elisa Colombo, Stefania Giussani, Elena Restelli, Eugenia Cammarota, Juan Manuel Battagliotti, Nikolai Klena, Moises Di Sante, Raghabendra Adhikari, Daniel Feliciano, Gaia Pigino, Elena Taverna, Oliver Harschnitz, Nicola Maghelli, Norbert Scherer, Damian Edward Dalle Nogare, Joran Deschamps, Francesco Pasqualini, Florian Jug Nature Methods · 2026 · DOI 10.1038/s41592-026-03082-1 Peer-reviewed article Bioimage analysis for multiplexed FUCCI acquisitions powered by deep learning J. Zimmermann, M. Pezzotti, E. Torchia, A. Enrico, M. Di Sante, F.S. Pasqualini npj Imaging · 2026 · DOI 10.1038/s44303-026-00159-6 Peer-reviewed article BIOPOINT: A particle-based model for probing nuclear mechanics and cell-ECM interactions via experimentally derived parameters Sandipan Chattaraj, Julius Zimmermann, Francesco Silvio Pasqualini PLOS Computational Biology · 2025 · DOI 10.1371/journal.pcbi.1014113 Peer-reviewed article An Open-Science Computational Model of Organelle Acidification to Integrate Putative Mechanisms of Synaptic Vesicle Acidification and Filling Baraglia EC, Fattorini G, Chattaraj S, Pasqualini F, Conti F Neurochemical Research · 2025 · DOI 10.1007/s11064-025-04432-9 Peer-reviewed article Molecular Dynamics Simulation of Structural Assembly and Hydration of Hyaluronic Acid in Salt Aqueous Buffer Vasudevan S, Chattaraj S, Enrico A, Pasqualini FS Langmuir · 2025 · DOI 10.1021/acs.langmuir.4c03966 Peer-reviewed article An efficient active-stress electromechanical isogeometric shell model for muscular thin-film simulations Torre M, Morganti S, Nitti A, de Tullio M D, Kiendl J, Pasqualini F S, Reali A Mechanics of Materials · 2024 Peer-reviewed article SEM2: Introducing mechanics in cell and tissue modeling using coarse-grained homogeneous particle dynamics Chattaraj S, Torre M, Kalcher C, Stukowski A, Morganti S, Reali A, Pasqualini FS APL Bioengineering · 2023 · DOI 10.1063/5.0166829 Peer-reviewed article muSplit: image decomposition for fluorescence microscopy Ashesh, Alexander Krull, Moises Di Sante, Francesco Silvio Pasqualini, Florian Jug IEEE/CVF International Conference on Computer Vision · 2023 · DOI 10.1109/iccv51070.2023.01940 Review Current progress toward isogeometric modeling of the heart biophysics Torre M, Morganti S, Pasqualini FS, Reali A Biophysical Reviews · 2023 · DOI 10.1063/5.0152690 Peer-reviewed article Isogeometric mixed collocation of nearly-incompressible electromechanics in finite deformations for cardiac muscle simulations Michele Torre, Simone Morganti, Alessandro Nitti, Marco D. de Tullio, Francesco S. Pasqualini, Alessandro Reali Computer Methods in Applied Mechanics and Engineering · 2023 · DOI 10.1016/j.cma.2023.116055 Peer-reviewed article Immersed isogeometric analysis based on a hybrid collocation/finite cell method Torre M, Morganti S, Pasqualini F S, Duster A, Reali A Computer Methods in Applied Mechanics and Engineering · 2023 Peer-reviewed article An efficient isogeometric collocation approach to cardiac electrophysiology Torre M, Morganti S, Nitti A, de Tullio M D, Pasqualini F S, Reali A Computer Methods in Applied Mechanics and Engineering · 2022 Peer-reviewed article A novel computational model of the human ventricular action potential and Ca transient Eleonora Grandi, Francesco S Pasqualini, Donald M Bers Journal of Molecular and Cellular Cardiology · 2010 · DOI 10.1016/j.yjmcc.2009.09.019 Peer-reviewed article Theoretical investigation of action potential duration dependence on extracellular Ca2+ in human cardiomyocytes Grandi E, Pasqualini FS, Pes C, Corsi C, Zaza A, Severi S Journal of Molecular and Cellular Cardiology · 2009 · DOI 10.1016/j.yjmcc.2008.12.002
Tools and resources
Useful links
BIOPOINT GitHub SPL repository for the BIOPOINT particle-based modeling workflow. SEM2 GitHub Subcellular Element Modeling and Mechanics code repository. DeepFUCCI GitHub Deep-learning analysis code for multiplexed FUCCI microscopy. Organelle acidification model Open-science ODE model repository for vesicle/organelle acidification.