About
An Interdisciplinary Image Analyst and PhD Physicist, enriched by practical knowledge from a core medicine career, who excels at turning complex visual data from any source into clear, measurable results. I apply advanced deep learning and physics-based modeling to solve novel problems across scientific and industrial sectors. My strength lies in designing custom, data-driven workflows and providing expert consultation to drive innovation, regardless of the specific field.
As a bioimage analyst with a unique foundation in both medicine and physics, I specialize in transforming complex visual data into precise, quantitative metrics. I bridge the gap between understanding intricate biological and geological systems and applying rigorous computational analysis to extract critical information.
My expertise delivers value across diverse industries:
Medical
Quantifying cellular features in histopathology and automating analysis for diagnostic and research applications.
Agricultural
Assessing crop health, analyzing root systems, and phenotyping from drone and microscopic imagery.
Petrography
Characterizing pore networks and quantifying mineral composition and grain structures in rock thin sections.I turn your images into objective data, enabling you to make better, faster, and more informed decisions. Let's connect via email to solve your imaging challenges.
Image Analyst
My primary focus is on developing image analysis pipelines to extract quantitative information, irrespective of the modality or area. My skills include proficiency in microscopy, encompassing the selection of appropriate techniques and the analysis and quantification of data to address various scientific inquiries. I always leverage the synergy between mathematical modeling and experiments to answer different questions effectively. I gain advantage of my interdisciplianry skillset to provide counselling regarding image analysis projects.
Beyond project execution, I am passionate about education and mentorship. I design and deliver customized courses for graduate, postgraduate, and industry settings on a wide range of subjects, including statistics, physics, image analysis and automation.
- Degree: PhD
- Website: acorbat.github.io
- Birthday: 18 January 1990
- Born in: Buenos Aires, Argentina
- Current City: Buenos Aires, Argentina
- Work email: acorbat.bia@gmail.com
- ORCID: 0000-0001-8068-3486
- GitHub: acorbat
- BlueSky: acorbat.bsky.social
PhD in Physics
During my PhD, I have been working under the advice of Dr. Hernán Grecco focusing on obtaining quantitative information from microscopy images to unravel how intra and intercellular signalling cascades emerge from underlying biological networks. To avoid experimenter bias and amass enough data, I worked on the design of experiments and programming of Python modules that would automatically analyze the acquired images. From this, I found out that microscopy, in all its variants, excels at determining individual characteristics in cell population providing essential information of their variability and subsequent behaviour.
Skills
In my pursuit of knowledge and expertise in the fields of physics, systems biology, and microscopy, I have honed a diverse skill set that is anchored in both scientific inquiry and technical proficiency. To automate processes and mitigate experimental bias, I ventured into programming, control and automation, and statistics. My commitment to integrating these skills into my work has enabled me to approach complex problems with a multidisciplinary perspective, fostering innovation and precision in scientific research and experimentation.
Portfolio
I applied the techniques I have learnt during this time to a plethora of different scientific questions gaining advantage on synergy between modelling and experiments to devise new questions. For example, I have studied the apoptotic signalling cascade where modelling the network led me to ask myself whether placing stimuli at different nodes of the network gives place to different dynamics. After designing the necessary experiments, I unraveled the role of key nodes in the apoptotic network and designed a single mathematical model to describe dynamics when applying different stimuli.
I have also worked with different image modalities, such as Magnetic Resonance Imaging and Video acuisitions, and diverse topics such as ecology and petrography.
- All
- Postdoctoral
- PhD
- Package
- Collaboration
- Image Analysis
Services & Materials
I provide Image Analysis freelance services to design and implement automatic pipelines and consultancy sessions. I also develop courses for academic and industry environments. Below you will find organized categories of teaching materials, educational resources, software tools, and best practice guides.
Teaching & Lectures
Video lectures and talks on bioimage analysis, microscopy, and artificial intelligence
Microscopy: Improve Your Imaging Skills
Course addressing theoretical and practical knowledge on experimental design in microscopy from sample preparation to image analysis.
Interfacing with Other Networks
Short talk on how bioimage analysts can interface between local communities and organizations.
On Navigating the Archipelago
Reflections on the diverse origins and backgrounds of bioimage analysts in the field.
Lecture Materials & Seminars
Documentation and materials for bioimage analysis seminars and workshops
Digital Image at CFMO
Foundational lecture on digital images in "Curso de Fundamentos de Microscopia Optica".
Introduction to BioImage Analysis at CFMO
Introductory material on image analysis techniques in microscopy courses.
AI Tools in Biology
Seminar on artificial intelligence and deep learning applications in bioimage analysis.
Image Analysis Lecture
Comprehensive introduction to image analysis techniques for researchers and PhD students.
Image Analysis Workshop
4-hour hands-on workshop teaching image analysis to PhD students and light microscopy users.
Educational Datasets
Image datasets designed for understanding microscopy challenges and their solutions
Uneven Illumination & Focus Dataset
Demonstrates effects of illumination and focus variations when stitching image tiles.
Bleedthrough & Saturation Dataset
Illustrates effects of bleedthrough, saturation, underexposure, and soft focus on image analysis.
Noise vs Averaging Dataset
Demonstrates the effects of noise levels on image analysis and the benefits of signal averaging.
Software & Tools
Python packages, code libraries, and automation tools for image analysis and scientific computing
img_manager
Python package with object wrappers for different microscopes and image correction algorithms.
Anisotropy Errors
Jupyter notebook exploring error propagation in anisotropy estimation calculations.
Teaching Examples
Notebooks for understanding goodness of fit through simulations and oscilloscope automation examples.
Liver Lineage Tracing
Simulation of lineage tracing systems using computational modeling and visualization.
Best Practices & Resources
Guidelines and documentation for organizing and managing scientific projects
Folder Convention Guide
Best practices for organizing project directories and file structures for reproducible research.
Publications
A selection of peer-reviewed publications from my research in bioimage analysis, biophysics, and systems biology. For a complete list and additional materials, refer to my detailed CV.
2025
Ectoderm barcoding reveals neural and cochlear compartmentalization
Science | DOI: 10.1126/science.adq9248
The non-canonical Smoothened-AMPK axis regulates Smaug1 biomolecular condensates
Journal of Cell Science | DOI: 10.1242/jcs.263433
2024
Jag1 represses Notch activation in lateral supporting cells and inhibits an outer hair cell fate in the medial cochlea
Development | DOI: 10.1242/dev.202949
Spatially segregated defects and IGF1-responsiveness of hilar and peripheral biliary organoids from a model of Alagille syndrome
Liver International | DOI: 10.1111/liv.15789
2023
Molten Globule Driven and Self-downmodulated Phase Separation of a Viral Factory Scaffold
Journal of Molecular Biology | DOI: 10.1016/j.jmb.2023.168153
2022
Smaug1 membrane-less organelles respond to AMPK and mTOR and affect mitochondrial function
Journal of Cell Science | DOI: 10.1242/jcs.253591
2021
An Integrative Apoptotic Reaction Model for extrinsic and intrinsic stimuli
bioRxiv (Preprint) | DOI: 10.1101/2021.05.21.444824
CASPAM: a triple modality biosensor for multiplexed imaging of caspase network activity
ACS Sensors | DOI: 10.1021/acssensors.1c00554
2018
Co-imaging extrinsic, intrinsic and effector caspase activity by fluorescence anisotropy microscopy
Redox Biology, Vol. 19, pp. 210-217 | DOI: 10.1016/j.redox.2018.07.023
Resume
In my career journey, I have had the unique opportunity to travel across the realms of medicine and physics, forging a multidisciplinary skill set that bridges the gap between biology and quantitative analysis. During my years in medical school, I learnt how variability in biology would arise at different levels, from the cellular level through tissue and organs to the whole individual. Upon embarking on my physics career, I intentionally selected biophysical and statistical elective courses to match my interest in quantitatively probing biological phenomena. This interdisciplinary journey has enabled me to seamlessly integrate my medical insights with advanced quantitative methodologies, fostering a unique skill set that enhances my ability to tackle complex scientific challenges at the intersection of physics and biology.
For a detailed CV, refer to overleaf.
Summary
Agustin Corbat
Physicist with a keen interest in image analysis and microscopy. Over 10 years of experience in image analysis, research and teaching, as well as programming and automating workflows.
- Buenos Aires, Argentina
- acorbat.bia@gmail.com
Professional Experience
BioImage Analyst
2025 - Present
Universidad de Buenos Aires, Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, UBA.
- At Instituto de Física de Buenos Aires (IFIBA).
- I provide support developing new image analysis pipelines or improving existing ones, as well as disseminating knowledge through courses.
BioImage Analyst
2024 - 2025
Uppsala Universitet, Uppsala, Sweden
- National Bioinformatics Infrastructure Sweden (NBIS) and SciLifeLab.
- At BioImage Informatics (BIIF).
- I provide support developing new image analysis pipelines or improving existing ones, as well as disseminating knowledge through courses.
Postdoctoral Researcher in Developmental Biology
2022 - 2024
Karolinska Institutet, Stockholm, Sweden
- Marie Skłodowska-Curie Action Seal Of Excellence - Awarded for excellence in research proposal and career development.
- My research was performed in Dr. Emma Andersson's Lab where I specialized in an interdisciplinary approach integrating microscopy and mathematical modeling to advance the field of developmental biology.
- My focus consisted on decoding the intricate interplay between Notch cell-to-cell signaling and mechanical forces, elucidating their role in precise pattern formation during inner ear development.
- Collaborated with colleagues in developing analysis of lineage tracing and microscopy images.
- Supervision of Master students.
Postdoctoral Researcher in Physics
2021 - 2022
Karolinska Institutet, Stockholm, Sweden
- Transitional postdoctoral position following PhD completion.
- Initial research orientation in physics-based approaches to biological imaging and modeling.
- Foundation for subsequent developmental biology research focus.
PhD Student
2016 - 2021
Universidad de Buenos Aires, Buenos Aires, Argentina
- National Scientific and Technical Research Council (CONICET) Postgraduate Fellowship to pursue a PhD 2016-2021, awarded through National competition.
- I pursued my PhD in Dr. Hernan Grecco's group where I applied microspectroscopy to quantification and modelling of signal propagation in biological networks.
- Collabroated with different groups to design microscopy experiment and image analysis pipelines.
- High Level Technological Service: Colaboration with Y-Tec, Digital Petrography, Image analysis and machine learning applied to gigapixel petrography samples.
Research Projects & Supervision
Research Project Contributions (2024-2025)
- Spatial Profiling of the Renal Host-Pathogen Interplay: Image analysis support for studying *Candida albicans* infection dynamics in mice using spatial transcriptomics and microscopy.
- MRI Segmentation of Cavernous Malformations: Deep learning approaches for automated segmentation of cavernous malformations in mouse brain MRI scans.
- Role of Perivascular TAM Phenotypes: Analysis of tumor-associated macrophage phenotypes and their role in metastatic dissemination.
- AI4Life Open Call 2 Projects: Contributed to artificial intelligence projects (#11 and #38) for advancing bioimage analysis capabilities.
Student Supervision & Mentoring
- Laboratorio 6 Student Project (2025-2026): Supervising undergraduate experiment on "How Microscope Capabilities Affect FRAP Parameter Estimation".
- Master's Student Supervision (2024): Mentoring graduate students in specialized image analysis techniques.
- High School Student Supervision (2024-2025): Guidance for advanced secondary education research projects.
Education
PhD. in Physics
2016 - 2021
Universidad de Buenos Aires, Buenos Aires, Argentina
Grade: 10 (grading scale: from 0 to 10, with 10 as maximum)
Advisor: Dr. Hernán E. Grecco; Defended on 10th of August of 2021
Thesis: Microspectroscopy applied to quantification and modelling of signal propagation in biological networks: I devised an integrative mathematical model for the apoptotic cascade by analyzing timing between caspases when using extrinsic and intrinsic stimuli.
Elective Subjects:
Licenciatura in Physical Sciences
2011 - 2016
Universidad de Buenos Aires, Buenos Aires, Argentina
General Average: 9.32, Historical Average: 8.51 (grading scale: from 0 to 10, with 10 as maximum). Estimated Time for Completion: 6 years. Actual Completion: 5 years
Thesis: Modelling Caspase Dynamics from Temporal Series: I theoretically calculated how to estimate protelytic activity from anisotropy polarization of homoFRET based biosensors and used three spectrally separated biosensors to monitor activity of extrinsic, intrinsic and effector caspases in time series of single cells.
Elective Subjects:
Medicine, Core Assignments Completed
2008 - 2010
Hospital Universitario Austral, Buenos Aires, Argentina
Merit Scholarship
General Average: 7.48 (grading scale: from 0 to 10, with 10 as maximum)
Professional Development & Training
Selected Advanced Courses & Workshops (2020-2024)
- Democratizing Microscopy in Latin America (2024, 50 hrs): Comprehensive workshop on microscopy techniques and bioimage analysis in Latin American context.
- Advanced Methods in Bioimage Analysis (2023, 50 hrs): EMBO workshop on cutting-edge bioimage analysis methodologies.
- Advanced Deep Learning with Transformers (2023, 16 hrs): Training in transformer architectures and attention mechanisms for image analysis.
- GPU Programming: Why, When and How? (2023, 16 hrs): EuroCC training on GPU acceleration for scientific computing.
- Quantitative Imaging: From Acquisition to Analysis (2018, 156 hrs): Cold Spring Harbor Laboratory intensive course with partial scholarship.
- School on Physics Applications in Biology (2018, 50 hrs): ICTP-SAIFR program with full support for studying physics in biological systems.
Teaching
Invited Lecturer
2025 | Fundacion Instituto Leloir, Buenos Aires, Argentina
- Introduction to Bioimage Analysis: Seminar and workshop introducing bioimage analysis techniques.
- Link to Material
2025 | Fundacion Instituto Leloir, Buenos Aires, Argentina
- Digital Image: Seminar and workshop on digital images.
- Link to Material
2025 | Swedish University of Agricultural Sciences, Uppsala, Sweden
- AI Tools in Biology: Seminar and workshop on artificial intelligence for bioimage analysis.
- Link to Material
2025 | Live Cell Imaging Facility, Karolinska Institutet, Stockholm, Sweden
- Microscopy: Improve Your Imaging Skills - From Sample Preparation to Image Analysis: Course addressing theoretical and practical knowledge on experimental design on microscopy.
- Link to video
- Link to Material
Teaching Assistant
2024 | Center for Cellular Imaging, Gothemburg University, Gothemburg, Sweden
- Introduction to Bioimage Analysis: Course addressing theoretical and practical knowledge on image analysis oriented to biology.
2024 | NBIS, Uppsala, Sweden
- Neural Nets and Deep Learning: Course addressing theoretical and practical knowledge on designing and understanding neural networks.
2024 | Karolinska Institutet, Stockholm, Sweden
- Microscopy: Improve Your Imaging Skills - From Sample Preparation to Image Analysis: Course addressing theoretical and practical knowledge on experimental design on microscopy.
2019 - 2021 | Universidad de Buenos Aires, Buenos Aires, Argentina
- Laboratory 3: Design, analysis and experimentation applied to electricity and magnetism. I was in charge of practical course.
Graduate Teaching Assistant
2017 - 2021 | Universidad de Buenos Aires, Buenos Aires, Argentina
- Control and Instrumentation: Design, signal processing, automation and instrumentation of various devices found in laboratories.
- Laboratory 5: Design, analysis and experimentation applied to different areas of physics.
- Laboratory 3: Design, analysis and experimentation applied to electricity and magnetism.
- Optical and Fluorescence Microscopy: Concepts and practice on design and experimentation with optical and fluorescence microscopes.
- Physics 1 for biologists and geologists: Mandatory classical mechanics and electromagnetism practical exercises for biologists and geologists.
Undergraduate Teaching Assistant
2015 - 2017 | Universidad de Buenos Aires, Buenos Aires, Argentina
- Physics 1 and 2 for biologists and geologists: Mandatory classical mechanics, electromagnetism, optics and thermodinamics practical exercises for biologists and geologists.
- Laboratory 1 for chemists: Classical mechanics and optics experiments for chemists.
- Laboratory 5: Design, analysis and experimentation applied to different areas of physics.
- Latex and Python Programming: 3 practical classes consisting of 3 hs. dictated once per semester. Organization, diffusion and presentation of the Workshop by students.
2010 | Hospital Universitario Austral, Buenos Aires, Argentina
Contact
You can contact me through my work email if you are interested in freelance consulting or GitHub if it is a matter regarding coding or a repository.