Scientist / Entrepreneur / Angel Investor

Bioimage analysis and AI across science, software, and company building.

Senior Staff Scientist and Co-head of Image and Data Analysis at ETH Zurich, independent consultant at Harvard Medical School, ex-CEO, serial entrepreneur, and investor working where Life Sciences meet Computer Science.

Worked in labs at ETH Zurich, Harvard Medical School, Humboldt University Berlin, MIT, and INRIA.

Co-founded companies including Tooploox Research, Histopixel, and Cat-astrophe Games.

Advised Bones Studio, MobilWay, and ZOWIE.

Szymon Stoma works at the multidisciplinary interface of Life Sciences and Computer Science, focused on bioimage analysis and artificial intelligence. His work connects advanced microscopy, data interpretation, AI-driven research workflows, consulting, and startup R&D.

Brief Bio

A condensed path through science, software, and company building.

2024-now Harvard Medical School Independent Consultant, Boston, USA

2016-now Histopixel CEO, Wroclaw, Poland

2014-now ETH Zurich Co-head of Image and Data Analysis, Zurich, Switzerland

2017-2024 Cat-astrophe Games Co-founder, Wroclaw, Poland

2013-2025 MicroscopeIT / Tooploox Research Co-founder and CEO, Wroclaw, Poland

2011-2014 INRIA Postdoc, Paris, France

2009-2011 Humboldt University Berlin Postdoc, Berlin, Germany

2005-2008 University of Montpellier / INRIA PhD, Montpellier, France

2000-2005 University of Wroclaw MSc, Wroclaw, Poland

Current Focus

Turning scientific images into decisions, systems, and useful software.

Scientific image analysis

Co-head of Image and Data Analysis at the Scientific Center for Optical and Electron Microscopy at ETH Zurich, supporting microscopy-centered research with quantitative image analysis and data interpretation.

AI R&D and company building

Ex-CEO of Tooploox Research, previously MicroscopeIT, a software house specializing in R&D, AI, and computer vision. He led the merger with Tooploox and later headed a 30+ person R&D department.

Interdisciplinary R&D consulting

Independent consulting at Harvard Medical School on DARTS, an ARPA-H-funded antibiotic resistance program led by the Paulsson Lab, focused on image analysis and data workflows for high-throughput bacterial mother-machine experiments.

Institutions

Academic labs and companies where the work left a trace.

Academic

ETH Zurich / ScopeM Co-head of Image and Data Analysis at ScopeM, building microscopy data workflows and collaborations across life science projects.

Harvard Medical School Worked in Johan Paulsson’s lab on DARTS, building image analysis and data workflows for high-throughput bacterial mother-machine experiments.

INRIA Worked in Grégory Batt’s InBio group on formal methods, systems biology, and dynamic cellular models; and with Christophe Godin on plant development.

MIT Worked in Ron Weiss’s lab on synthetic circuits leading to tissue homeostasis and the variability of cell populations.

Humboldt University Berlin Worked in Edda Klipp’s Theoretical Biophysics group on modeling and the wet/dry lab interface.

Founded Companies

Tooploox Research / MicroscopeIT Co-founder and CEO of MicroscopeIT, an AI R&D software house later merged into Tooploox Research.

Histopixel Founder of Histopixel, a consulting vehicle for scientific image analysis, AI, microscopy, and pharma-facing R&D; see KRS 0000663706.

Cat-astrophe Games Co-founder of Cat-astrophe Games, an indie studio specializing in AR/VR technologies and game production.

Selected Activities

Projects, communities, investments, and shipped work.

2024

Don't Be Afraid 2

Co-producer of the game sequel, released on Steam by Eneida Games and Cat-astrophe Games.

2020-2026

BONES-SEED

Strategic R&D advisory work behind motion-data infrastructure later reflected in BONES-SEED, linked to the Bones Studio robotics data stack.

2020-now

Angel investing

ZOWIE, MobilWay S.A., and early seed-phase ventures.

2020-2024

Essential Vision

Co-founder of Essential Vision, an open-source mixed-reality platform for teaching anatomy, simulation, and visual models.

2017-now

ZIDAS

Co-founder of an international school on image and data analysis for life scientists; see zidas.org.

2016-now

Bioimage analyst networks

Co-founding and community work across SwissBIAS, NEUBIAS, and GloBIAS, connecting analysts, training, and open resources.

2015-2019

CellStar

Co-founder of CellStar and the Evaluation Platform for long-term tracking of budding yeast cells.

2009-2020

STSE

Founder and main developer of STSE, the Spatio-Temporal Simulation Environment for biological modeling, image-derived geometry, and simulation.

2010-2018

Yeast Image Toolkit

Founder of the Yeast Image Toolkit, a software collection for yeast microscopy image analysis.

Selected Hands-On Examples

Things I modeled, simulated, or programmed directly.

Simulation frame of a growing meristem model

INRIA / PhD Growing meristem

Auxin transport, mechanics, and phyllotactic pattern formation in a simulated meristem.

HU Berlin / Postdoc Aquaporin dynamics

Postdoc-era modeling work around membrane transport and plant-development mechanisms.

Three-dimensional tissue image analysis preview

INRIA / Postdoc Tissue reconstruction

Volumetric image analysis and reconstruction of complex biological tissue.

GOL-style multi-agent simulation preview

MIT / Visiting Scientist GOL simulation

Multi-agent growth simulation connecting rule-based dynamics with image-analysis thinking.

Yeast colony growth and tracking preview

MIT / Visiting Scientist Yeast colony

Segmentation, tracking, and growth analysis for microscopy time-lapse data.

Thumbnail for the Essential Vision teaser video

ETH / Staff Scientist Essential Vision

Mixed-reality anatomy, simulation, and guided-learning work for HoloLens-style teaching environments.

Selected Publications

A few anchors from the archive.

2024 OME-NGFF workflows hackathon Luthi J et al., BioHackrXiv, 2025
Quantitative spatial analysis of hematopoiesis-regulating stromal cells Gomariz A et al., Nature Communications, 2018
AutoTube: automated morphometric analysis of vascular networks Montoya J et al., Angiogenesis, 2018
STL-based analysis of TRAIL-induced apoptosis Stoma S and Donze A et al., PLoS Computational Biology, 2013
Flux-Based Transport Enhancement in Meristem Development Stoma S et al., PLoS Computational Biology, 2008

Selected Teaching

Courses and workshops in bioimage analysis, AI, and scientific computing.

2022-now Bioinformatics ETH Zurich 2016-now Zurich Image and Data Analysis School SwissBIAS / ZIDAS 2020-2021 Deep Learning for Bioimage Analysis EMBL Heidelberg

2016-2023 Microscopy Summer School Center for Experimental and Clinical Imaging Technologies Zurich

2009-2012 Python, Matlab, modeling, and scientific programming Humboldt University Berlin and earlier teaching

Available For

Advisory, board, scientific board, and public speaking roles around ambitious technical projects.

Open to conversations about thoughtful work at the edge of bioimage analysis, AI, life sciences, pharma, robotics, and company building. Best reached via LinkedIn.