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
I provide Image Analysis freelance services to design and implement automatic pipelines and consultancy sessions. I also develop courses for academic and industry environments. You can find below some of the materials I produced.
Interfacing with other networks
Short talk delivered at GloBIAS in-person workshop about how GloBIAS could interface between local communities.
On Navigating the Archipelago
Short talk delivered at GloBIAS in-person workshop about where bioimage analysts come from.
Digital Image at CFMO
Lecture introducing to digital images in Curso de Fundamentos de Microscopia Optica.
Introduction to BioImage Analysis at CFMO
Lecture introducing to image analysis in Curso de Fundamentos de Microscopia Optica.
Image Analysis Workshop
This 4h workshop intends to teach image analysis to PhD students and researchers who acquire light microscopy images.
Correction of Uneven Illumination and Uneven Focus Dataset
Image dataset with the goal of demonstrating the effect of uneven illumination or uneven focus when stitching tiles.
Bleedthrough, Saturation/Underexposure and Soft Focus Dataset
Image dataset with the goal of demonstrating the effect bleedthrough, saturation, underexposure or soft focus on image analysis.
Noise Level versus Averaging Dataset
Image dataset with the goal of demonstrating the effect of noise on image analysis.
Teaching examples
Conatins a notebook to understand goodness of fit through simulations. And a small example of automation for osciloscopes.
img_manager
A Python package with Object wrappers for different microscopes and image correction algorithms.
Liver Lineage Tracing
A small notebook to simulate a system similar to the one proposed by Unterweger et al.
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
2021 - 2024
Karolinska Institutet, Stockholm, Sweden
- Marie Skłodowska-Curie Action Seal Of Excellence.
- 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 devoloping analysis of lineage tracing and microscopy images.
- Supervision of Master students.
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.
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)
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.