I am an applied AI/ML researcher specialized in machine learning and software automation to accelerate decision-making in biomedical research.
I am the principal developer of Goo, a one-stop software to simulate cell mechanics, molecular communication and gene regulatory networks in 3D inside Blender.
I research on image analysis and computer vision models to make sense of high-dimensional datasets of microscopy images.
I teach several workshops about digital image analysis at Harvard Medical School. The QuPath workshop is back this semester! More info.
I strive for research so beautiful it is mistaken for art, and art so technical it is mistaken for science.
My formal education is in Bioengineering and in Bioinformatics. As for my research, it has spanned: machine learning for genome mining, computer vision for microscopy image analysis, 3D simulation of embryonic development, and medical device development for remote tissue evaluation.
I joined Harvard University as a Computational Biologist in 2023, after spending a year as a Visiting Researcher in the Department of Systems Biology. Previous to that, I researched for a year in the Laboratory for Biomolecular Discovery and Engineering at KU Leuven as a Machine Learning Researcher.
Favorite tools:
Teaching in Pune, India
I will be teaching bioimage analysis with Python at the 2025 Global BioImaging Image Data Course at IISER Pune, India.
Papers out!
Our work on studying the spatial distributions of cell markers in stroma-rich tumors, highlighting the role of NRDG1 in pancreatic ductal adenocarcinoma is now available on bioRxiv: Kozlova et al., 2025; Ruzette et al., 2025
2025 Janelia AI Conference
I presented my work on large synthetic datasets to train foundation models for bioimage analysis at the 2025 AI Revolution Meets 4D Cellular Physiology conference at HHMI Janelia. Watch the recording here.
2024 Bisconti Award
My project on large synthetic datasets to train foundation models for cell segmentation was awarded with the 2024 Bisconti Award ($50.000) by the Core for Computational Biomedicine at Harvard University.
2023 Blender Conference
I gave a talk at the 2023 Blender Conference in Amsterdam about my research on simulating cells and tissues in 3D. Watch the recording here.
Moving to Boston, MA
I joined the groups of Prof. Sean Megason and Dr. Simon Nørrelykke (Image Analysis Collaboratory) at Harvard Medical School as an Associate in Systems Biology.
antoine_ruzette AT hms.harvard.edu
