Lucien Hinderling

Tries to make microscopes smarter 		Hello! github bsky twitter email
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Hi there!!

I’m a cell biologist with a background in computer science, working on real-time feedback control microscopy at the University of Bern. Here’s a 3-min video or 40-min talk presenting my work.

From 2027, I’m starting a lab at EMBL Heidelberg, taking microscopes from automation to autonomy: from machines that follow instructions to systems that can explore, learn, and decide what to do next. Our long-term vision is a laboratory that can design and run its own experiments. If you are excited about bringing the success of agentic AI in coding and maths to experimental biology, let’s chat!

Research

Smart microscopy

During my PhD in Pertz Lab I built an experimental platform for closed-loop, feedback control microscopy. We primarily use the platform for optogenetic experiments, where we segment and track cells in real-time to automatically generate stimulation masks with sub-cellular precision. This technology allows us to manipulate cells with remarkable accuracy, and for example steer them around like tiny biologcial remote-controlled cars. We can control hundreds of cells simultaneously, enabling unprecedented experimental throughput (see preprint|code).

Movie: Automated optogenetic control of hundreds of cells in parallel. Each cell is individually steered, collectively acting as a “tissue printer”. 
╭──────────────────────────────╮
│ User                         │
╰──────────────────────────────╯
    ↕          ↕          ↕
┌────────┐ ┌────────┐ ┌────────┐
│ GUI    │ │ CODE   │ │ LLM    │
│ napari │ │ python │ │        │
└───┬────┘ └───┬────┘ └───┬────┘
┌───┴──────────┴──────────┴────┐
│ Microscope Control Software  │
│ uManager/pymmcore            │
└──────────────┬───────────────┘
┌──────────────┴───────────────┐
│ Microscope Hardware          │
│ camera/stage/filters/DMD/... │
└──────────────────────────────┘
               ↕
╭──────────────────────────────╮
│ Live Cells                   │
│ biosensors/optogenetics      │
╰──────────────────────────────╯
Diagram: Architecture of feedback control microscopy platform.

As member of the Smart Microscopy Working Group, I am interested to standardize adaptive feedback microscopy workflows, working with experts from academia and industry to create reference specifications for consistent implementation and reproducibility across imaging systems (see paper).

I use LLMs as an interface between users and microscope hardware, to simplify the control of these complex machines and enable automation tasks that require reasoning on experimental output. As agentic AI becomes more and more powerful, the question is how far this can go: from microscopes that follow our instructions to microscopes that decide what to do next.

From automation to autonomy

My goal is a laboratory that designs and runs its own experiments. I see this as a ladder of autonomy: agents that (i) translate natural-language requests into microscope control code, (ii) set up and run feedback-control experiments on demand, and (iii) plan experiments towards a scientific goal and decide on the next one themselves. As there is no training data of researchers operating instruments, we let agents learn in a simulated lab, where one agent builds virtual microscopes and challenges and another solves them. Skills learned this way already transfer to real microscopes. At EMBL we will scale this up and build the agent-ready environment (connected devices, shared standards, structured metadata) it needs.

  Write code      Control      Run feedback         Autonomous
                  hardware     experiments           planning
╭────────────╮ ╭────────────╮ ╭────────────╮ ╭──────────────────────╮
│    User    │ │    User    │ │    User    │ │         User         │
│     ↓      │ │     ↓      │ │     ↓      │ │          ↓           │
│    LLM     │ │    LLM     │ │    LLM     │ │         LLM          │
│     ↓      │ │     ↓      │ │     ↕      │ │      ↙   ↕    ↘      │
│  Computer  │ │ Microscope │ │Scope+Cells │ │ Models Robots Scopes │
╰────────────╯ ╰────────────╯ ╰────────────╯ ╰──────────────────────╯
Diagram: Ladder of autonomy, from writing code to autonomous experiment planning.

Image analysis

Passionate about all things bio-image analysis, I’m especially proud of Convpaint, an interactive pixel classification tool we developed. It uses pretrained ViTs to extract image features. With a simple GUI in napari, users can train an ML model in seconds to identify structures in cells and tissues, or even track animal behavior. Convpaint seamlessly handles multidimensional data (time-series, 3D, multichannel). Paper now out in Cell Reports Methods. Want to try it out? Either the docs or 2h video recording of a workshop (I2K conference) are good starting places.

Movie: Visualisation of collective MCF10A cell movement.

Cellular signalling

Using diverse experimental approaches (fluorescent biosensors, optogenetics, microfabrication), I’m investigating cellular signaling dynamics, primarily at the subcellular scale. I’m fascinated by self-organizational properties at the interface between active matter and life.

Movie: A rat cell squeezing through micro-channel, 3D printed on a microscope with custom code and protocols.

Selected publications

All papers: google scholar
Year Title Links
2025
1st 		Real-time feedback control microscopy for automation of optogenetic targeting [bioRxiv]
L Hinderling, AE Landolt, B Graedel, L Dubied, C Zahni, A Frismantiene, T Lambert, M Dobrzynski, O Pertz 		preprint
code
2026
1st 		Smart Microscopy: Current Implementations and a Roadmap for Interoperability [Methods in Microscopy]
L Hinderling, HS Heil, A Rates, P Seidel, M Gunkel, B Diederich, […], O Pertz, N Norlin, A Halavatyi, R Camacho 		paper
press a
press b
website
2025
1st 		Teach your microscope how to print: low-cost and rapid-iteration microfabrication for biology [Lab on a Chip]
L Hinderling, R Hadorn, M Kwasny, J Frei, B Grädel, S Psalmon, Y Blum, R Berthoz, AE Landolt, BD Towbin, D Riveline, O Pertz 		paper
code
2026
1st 		Convpaint - Interactive pixel classification using pretrained neural networks [Cell Reports Methods]
L Hinderling, G Witz, R Schwob, A Stojiljkovic, M Dobrzyński, M Vladymyrov, J Frei, B Grädel, A Frismantiene, O Pertz. 		paper
code
2026
co-1st 		GTPase activating protein DLC1 spatio-temporally regulates Rho signaling [eLife]
L Hinderling, M Heydasch, J van Unen, M Dobrzynski, O Pertz 		paper 
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Selected talks

Year Event Location
2026 AI Lund SE, Lund
2026 Crick BioImage Analysis Symposium UK, London
2026 EPFL BioImaging and Optics Core Facility seminar CH, Lausanne
2026 STRADA Conference CH, Bern
2026 SwissBIAS annual meeting CH, Bern
2026 Euro-BioImaging Virtual Pub
VIDEO RECORDING 		Virtual
2026 Graduation ceremony, University of Bern
Awarded faculty price for best PhD thesis 		CH, Bern
2026 MNB course, D-BSSE Basel CH, Basel
2026 RTmfm SMILE seminar
VIDEO RECORDING 		Virtual
2025 Institut Curie FR, Paris
2025 BNMI Symposium SE, Gothenburg
2024 I2K Image to Knowledge Conference IT, Milan
2024 AI Lund Smart Microscopy hackathon SE, Lund
2024 XI Seminar on Extended Intelligence, Data Science Lab CH, Bern
2023 Librehub LatAm
VIDEO RECORDING 		CL, Chile (virtual)
2023 Cytomeet conference
Awarded best junior presentation 		CH, Bern
2022 Nacht der Forschung CH, Bern
2022 InSiDE Optogenetics Workshop
Talk and co-organization of workshop 		Virtual
2021 naXys, Namur Institute for Complex Systems BE, Namur (virtual) 
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Art in research

How can methods from art practices be applied to research, and how can research be communicated through art? Works resulting from interdisciplinary collaboration (Photography Tim Oliver Rod, Music Ueli Kempter) have been exhibited in galleries and are used in scientific presentations. A video has recently been awarded by the Swiss National Science Foundation (press release).

┌─────────┐  ┌────────┐  ┌────────────┐
│Bio image│─►│Analysis│─►│Sonification│
└──┬──────┘  └────────┘  └──┬─────────┘
   │ video                  │ ♪ sound 
   │         ╭────────╮     │ 
   └────────►│ User   │◄────┘
             ╰────────╯
Diagram: Results of image analysis are converted to sound. Users can process more information by using multiple senses. Some data is better perceptible by ear, such as changes in oscillation frequencies.
Year Exhibition Location
2025 Choreography of migrant tumor cells
Video loop, showing microscopy and data analysis. Awarded jury distinction by Swiss National Science Foundation (SNSF) 		Journées photographiques de Bienne
2023 Where is Paradise?
Collab. with Tim Rod, interactive installation and AI photography 		Cantonale Bern-Jura la Nef
2023 Urgent Paradise
Collab. with Tim Rod & Timothée Verheij, interactive sound installation and AI photography 		CabaneB Bern
2023 (no title)
Piece in exhibition by Selina Lutz. Collabo. with Ueli Kempter, Single-cell movie and data sonification 		Lokal-Int Biel
2023 Urgent Paradise
Collabo. with Tim Rod & Timothée Verheij, interactive sound installation and AI photography 		Strates Gallery Lausanne
2023 Urgent Paradise
Collab. with Tim Rod, interactive installation and AI photography 		Reflector Contemporary Art Gallery
Photo: Training ML models to generate floating palm trees. Iv’e later used the same algorithms to halucinate microscopy data to train cell segmentation models.
Photo: 1/400 postcards exhibited in Urgent Paradise.
Description of postcard series

The postcard series “Greetings from Paradise” features a palm tree-lined, abandoned pool, where the stagnant water reflects the surrounding plants in a blurry way. The work is based on a photograph by Tim Rod, also exhibited in the gallery, and shows 400 variations on the theme. These variations subtly shift collective spaces of experience by combining Rod’s original image with similar photographic motifs from the internet, modifying and multiplying them. Through this altered repetition, a connection is made with the replication of tourist perspectives, traditionally sold through standardized postcard images. However, newer forms of tourist photography and memory-making are also addressed by incorporating filters influenced by temporal and subjective nuances of imagery. These newer forms are increasingly used as templates for followers on contemporary visual media channels and the algorithms linked to them.
Text adapted from Christina Irrgang

Photo: Gallery view Strates, Lausanne (2023).
Photo: Street view of installation Perpetual Sunset, Reflector Gallery, Bern (2023). 
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Funding

Thank you to the organizations that supported this work: Swiss National Science Foundation (SNSF), Chan Zuckerberg Initiative (CZI) [Convpaint], University of Bern (Digitalisation Committee, Faculty of Science), and everyone who backed FabScope on experiment.com.

Short CV

Year Education
2027– Team leader, EMBL Heidelberg
Smart microscopy and agentic research. Taking microscopes from automation to autonomy.
2025–2026 Postdoc, University Bern
Natural language control of microscopes and wrapping up PhD projects.
2021–2025 PhD in Quantitative Cell Biology, University Bern
Thesis: Development of feedback-control microscopy workflows, microscope automation, machine learning, computer vision, and cell biology.
2019–2021 MSc in Bioinformatics & Computational Biology, University Fribourg & Bern
Thesis: Image processing pipeline for cell segmentation and tracking. Practicals on molecular biology and bioinformatics.
2015–2019 BSc in Computer Science, University Fribourg
Thesis: Image processing tools for hyperspectral UAV images. Minor in Environmental Science. Bilingual: French & German.
Year Work
2021–2023 Head of ICT Campus Bern, ICT Scouts / Campus
Supervised a team of 5, managed campus operations, coordinated workplans, communicated with parents, and helped establish the girls* club.
2019–2021 Talent scout & coach, ICT Scouts / Campus
Scouting and support of young ICT talents. Teaching coding (scratch, python, HTML & CSS), arduino, robotics, 3D printing.
2016–2019 Scientific assistant, University Bern
Field work at Institute of Plant Ecology (PANDIV, SADE, DFG).
2017–2021 Youth worker, Day School Lorraine Bern
Childcare for ages 4–13.
2012–2018 Custodian, Resident Community Münsingen
Cleaning and minor repairs. 
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