Agustin Corbat

I'm

About

I am a versatile physicist with a strong passion for problem-solving and a keen interest in interdisciplinary research. 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 biological data to address various scientific inquiries. I always leverage the synergy between mathematical modeling and experiments to answer different questions effectively. In addition to my research abilities, I have a deep love for teaching and have successfully imparted knowledge in subjects ranging from statistics and physics to control and automation, as well as laboratory work, to both physics and biology students.

If you have any questions or would like to get assisstance for a project, feel free to reach out to me via mail.

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.

  • Degree: PhD
  • Website: acorbat.github.io
  • Birthday: 18 January 1990
  • Born in: Buenos Aires, Argentina
  • Current City: Stockholm, Sweden

Bioimage Analyst

As a Bioimage Analyst in BioImage Informatics (BIIF) at SciLifeLab and Uppsala Universitet. I gain advantage of my interdisciplianry skillset to provide counselling regarding image analysis projects. Here, I provide support developing new image analysis pipelines or improving existing ones, as well as disseminating knowledge through courses.

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.

Python100%
Image Analysis 90%
Mathematical Modeling 80%
Microscopy 95%
Systems Biology 75%
Cell and Molecular Biology 70%

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 research and teaching, as well as programming and automating workflows.

  • Stockholm, Sweden
  • acorbat.bia@gmail.com

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:

  • Biology of Molecular Systems: Modelling and experimental validation of biological networks.
  • Optical and Fluorescence Microscopy: Theoretical and practical course regarding many aspects of microscopy and image acquisition.
  • Fourier Optics: Theoretical course treating Fourier optics.
  • Machine Learning: Theroetical and hands on course regarding various machine learning aspects and examples.
  • Electronics Laboratory: Design, analysis and experimentation with diverse circuits.

    • 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:

  • Topics in Molecular Biophysics: General concepts regarding biochemistry and biology with experiments regarding measurements of biophysical values.
  • Biophysics: Theoretical course regarding modelling of diverse biological systems.
  • Experimental Uncertainties and Theory of Error: Advanced statistics course.

    • 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 Experience

    BioImage Analyst

    2024 - Present

    Uppsala Universitet, Uppsala, Sweden

    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.

    Teaching

    Teaching Assistant

    2025 | Swedish University of Agricultural Sciences, Uppsala, Sweden

    • AI Tools in Biology: Seminar and workshop on artificial intelligence for bioimage analysis.

    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

    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

  • Cellular and Molecular Medicine: Preparation and presentation of Molecular Biology practical lessons for Medicine undergraduate students.

    • Portfolio

    I applied the techniques I have learnt during this time to a plethora of different biological 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.

    • All
    • Postdoctoral
    • PhD
    • Package
    • Collaboration
    • Image Analysis

    Services

    Teaching and random packages. Work in progress...

    Folder Convention

    A suggestion on how to organize project folders

    Anisotropy Errors

    A notebook to get immersed into how errors propagate in anisotropy estimation.

    Teaching examples

    Conatins a notebook to understand goodness of fit through simulations. And a small example of automation for osciloscopes.

    Adjutant

    A small AI chatbot for slack capable of remotely waking up computers through wake-on-LAN.

    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.

    Radiobiologia

    A small notebook to play around with Linear Quadratic Model in Radiobiology.

    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.