Lucien Hinderling

Tries to make microscopes smarter 		Hello! Contact
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Hi there!!

I’m a cell biologist with a background in computer science, developing real-time feedback control microscopy approaches at the University of Bern.

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.

╭──────────────────────────────╮
│ User                         │
╰──────────────────────────────╯
    ↕          ↕          ↕
┌────────┐ ┌────────┐ ┌────────┐
│ GUI    │ │ CODE   │ │ LLM    │
│ napari │ │ python │ │        │
└───┬────┘ └───┬────┘ └───┬────┘
┌───┴──────────┴──────────┴────┐
│ Microscope Control Software  │
│ uManager/pymmcore            │
└──────────────┬───────────────┘
┌──────────────┴───────────────┐
│ Microscope Hardware          │
│ camera/stage/filters/DMD/... │
└──────────────────────────────┘
               ↕
╭──────────────────────────────╮
│ Live Cells                   │
│ biosensors/optogenetics      │
╰──────────────────────────────╯
Figure: Architecture of feed-back control microscopy platform.

A current project explores how LLMs can interface between users and microscope hardware, to simplify the control of these complex machines and enable complex automation tasks that require reasoning on experimental output.

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.

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).

Cellular signalling

Using diverse experimental approaches (fluorescent biosensors, optogenetics, micro-fabrication), 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.

Publications

Year Title Link
2024
1st 		Convpaint - Interactive pixel classification using pretrained neural networks
L Hinderling, G Witz, R Schwob, A Stojiljkovic, M Dobrzyński, M Vladymyrov, J Frei, B Grädel, A Frismantiene, O Pertz 		bioRxiv
2024 Feedback regulation by the RhoA-specific GEF ARHGEF17 regulates actomyosin network disassembly
V Rao, B Gradel, L Hinderling, J van Unen, O Pertz 		bioRxiv
2024 Transformer-based spatial–temporal detection of apoptotic cell death in live-cell imaging
AP Gagliardi, DU Pizzagalli, PA Gagliardi, L Hinderling, P Lopez, R Zayats, PC Barberà, P Antonello, MP Segura, B Grädel, M Nicolai, A Giusti, M Thelen, LM Gambardella, TT Murooka, O Pertz, R Krause, SF Gonzalez 		elife
2023 Automatic detection of spatio-temporal signaling patterns in cell collectives
PA Gagliardi, B Grädel, MA Jacques, L Hinderling, P Ender, AR Cohen, G Kastberger, O Pertz, M Dobrzyński 		JCB
2023
co-1st 		GTPase activating protein DLC1 spatio-temporally regulates Rho signaling
M Heydasch, L Hinderling, J van Unen, M Dobrzynski, O Pertz 		bioRxiv
2022 LITOS: a versatile LED illumination tool for optogenetic stimulation
TC Höhener, AE Landolt, C Dessauges, L Hinderling, PA Gagliardi, O Pertz 		Scientific Reports 
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Selected talks

Year Title Event
2024 Smart Microscopy - automation of imaging experiments and active learning.
Invited talk, XI Seminar - Seminar on Extended Intelligence 		Data Science Lab
2024 Feedback-control microscopy.
Flash talk and poster, AI and Biology Symposium 		EMBL
2023 Hardware control and smart microscopy approaches in Napari.
Invited talk for Librehub LatAm. VIDEO RECORDING 		LIBREhub
2022 RhoA dynamics in shape oscillations and blebbing.
Award for Best Junior Presentation. 		Cytomeet conference
2022 Wie man Zellen mit Licht fernsteuern kann.
Public outreach event 		Nacht der Forschung
2022 Optogenetics workshop: from the fundamentals to the cutting edge.
Talk and co-organization of workshop 		Signaling Dynamics & Encoding
2021 Exploring emergent behaviours in epithelia using feedback-control microscopy
BeFri Research Colloquium 		$X....xX$$ .Xx.....+x +XX$X:....
2021 Live or die: Controlling the fate of cells in a tissue in real time using feedback- control microscopy
Invited talk at Namur institute for complex systems 		naxys 
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Art in Research

I’m interested in how art methods can be applied to research and how research can 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.

┌─────────┐  ┌────────┐  ┌────────────┐
│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
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 Bern
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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