Lucien Hinderling
@lhinderling.bsky.social
tries to make microscopes smarter · bioimage analysis, optogenetics, ml, 3d printing, open science · phd student in cellular signalling dynamics @PertzLab
quick test with SAM3 - impressed with how well it seems to track long protrusions? prompted for "cell", does not find anything when looking for "fibroblast" or "nucleus"
November 19, 2025 at 8:15 PM
quick test with SAM3 - impressed with how well it seems to track long protrusions? prompted for "cell", does not find anything when looking for "fibroblast" or "nucleus"
Last-minute advert for the Convpaint workshop at I2K by Roman Schwob! Interactive segmentation in @napari.org. Today 2:00 PM CET. Free registration:
www.i2kconference.org/workshops
www.i2kconference.org/workshops
November 18, 2025 at 12:13 PM
Last-minute advert for the Convpaint workshop at I2K by Roman Schwob! Interactive segmentation in @napari.org. Today 2:00 PM CET. Free registration:
www.i2kconference.org/workshops
www.i2kconference.org/workshops
Working on it!! You extract all the hardware (DMD+UV LED) from a consumer 3D printer for $300, while Mightex is 30k... Early tests below, showing how we can increase the printing resolution by changing the optics. Using an inverted vintage canon camera lens as objective 😅
October 26, 2025 at 5:41 PM
Working on it!! You extract all the hardware (DMD+UV LED) from a consumer 3D printer for $300, while Mightex is 30k... Early tests below, showing how we can increase the printing resolution by changing the optics. Using an inverted vintage canon camera lens as objective 😅
microfabricated stamps, fresh off the printer :)
October 26, 2025 at 4:24 PM
microfabricated stamps, fresh off the printer :)
Want to get started with smart microscopy? 🧠🔬
Check out our online repository with implementations from labs and industry -- lots of practical tips and links to sample code! smartmicroscopy.github.io/implementati...
More details in the ✨updated preprint!✨
www.biorxiv.org/content/10.1...
Check out our online repository with implementations from labs and industry -- lots of practical tips and links to sample code! smartmicroscopy.github.io/implementati...
More details in the ✨updated preprint!✨
www.biorxiv.org/content/10.1...
October 1, 2025 at 9:43 AM
Want to get started with smart microscopy? 🧠🔬
Check out our online repository with implementations from labs and industry -- lots of practical tips and links to sample code! smartmicroscopy.github.io/implementati...
More details in the ✨updated preprint!✨
www.biorxiv.org/content/10.1...
Check out our online repository with implementations from labs and industry -- lots of practical tips and links to sample code! smartmicroscopy.github.io/implementati...
More details in the ✨updated preprint!✨
www.biorxiv.org/content/10.1...
seems to also contain a lot of useful IO/processing/filtering functions i find myself reimplementing again and again across projects
mannlabs.github.io/scPortrait/i...
mannlabs.github.io/scPortrait/i...
September 28, 2025 at 8:28 PM
seems to also contain a lot of useful IO/processing/filtering functions i find myself reimplementing again and again across projects
mannlabs.github.io/scPortrait/i...
mannlabs.github.io/scPortrait/i...
I think we see similar adaption with DLC1 (a RhoA GEF) -- super cool to see this systematically investigated! After adaption, we see the strongest differences with acute perturbations. Cells can recover high-level functions, but differences persist at lower scales? elifesciences.org/reviewed-pre...
August 22, 2025 at 11:40 AM
I think we see similar adaption with DLC1 (a RhoA GEF) -- super cool to see this systematically investigated! After adaption, we see the strongest differences with acute perturbations. Cells can recover high-level functions, but differences persist at lower scales? elifesciences.org/reviewed-pre...
Each experiment gets a jupyter notebook, so experiments are reproducible and easy to run, even for users with little coding experience. Image processing pipeline is modular, easily adjusted to different cell lines or experiments. Using @napari.org as GUI. Code: github.com/pertzlab/rtm...
August 21, 2025 at 8:16 PM
Each experiment gets a jupyter notebook, so experiments are reproducible and easy to run, even for users with little coding experience. Image processing pipeline is modular, easily adjusted to different cell lines or experiments. Using @napari.org as GUI. Code: github.com/pertzlab/rtm...
Platform builds on open source software, compatible with hundreds of devices (µManager based, everything controlled from python thanks to pymmcore-plus). Worked so well, we started applying to all the projects in the lab -- from subcellular to tissue scale. Lots of examples in the paper.
August 21, 2025 at 8:16 PM
Platform builds on open source software, compatible with hundreds of devices (µManager based, everything controlled from python thanks to pymmcore-plus). Worked so well, we started applying to all the projects in the lab -- from subcellular to tissue scale. Lots of examples in the paper.
Automated optogenetic control of hundreds of cells in parallel. Each cell is individually steered, collectively acting as a "tissue printer". Preprint & code out! www.biorxiv.org/content/10.1...
August 21, 2025 at 8:16 PM
Automated optogenetic control of hundreds of cells in parallel. Each cell is individually steered, collectively acting as a "tissue printer". Preprint & code out! www.biorxiv.org/content/10.1...
So many people involved! Special thanks to @hannah-superres.bsky.social, Alfredo Rates, @olivierpertz.bsky.social, @nilsnorlin.bsky.social, Aliaksandr Halavatyi & Rafael Camacho. Link again to the paper: www.biorxiv.org/content/10.1...
August 21, 2025 at 2:22 PM
So many people involved! Special thanks to @hannah-superres.bsky.social, Alfredo Rates, @olivierpertz.bsky.social, @nilsnorlin.bsky.social, Aliaksandr Halavatyi & Rafael Camacho. Link again to the paper: www.biorxiv.org/content/10.1...
Here's @hannah-superres.bsky.social announcing the paper on stage at the BNMI conference. Came out 10 minutes before her talk started 😅🚀 Also check out her thread: bsky.app/profile/hann...
August 21, 2025 at 2:22 PM
Here's @hannah-superres.bsky.social announcing the paper on stage at the BNMI conference. Came out 10 minutes before her talk started 😅🚀 Also check out her thread: bsky.app/profile/hann...
Barriers are not only technical, but also hindered by structural/systemic challenges: academic reward system, vendor lock-in... Call to action! Join the smart microscopy working group to collaborate, share resources, define common standards. smartmicroscopy.github.io
August 21, 2025 at 2:22 PM
Barriers are not only technical, but also hindered by structural/systemic challenges: academic reward system, vendor lock-in... Call to action! Join the smart microscopy working group to collaborate, share resources, define common standards. smartmicroscopy.github.io
We end the paper with our vision for the future of smart microscopy: A modular, open and interoperable ecosystem 🤝
August 21, 2025 at 2:22 PM
We end the paper with our vision for the future of smart microscopy: A modular, open and interoperable ecosystem 🤝
Diverse approaches exist! The code is often hidden in the suppl. info, so we created an online database, with links to code repos and practical info. We collect 10 implementations of smart microscopy workflows from industry and academia: smartmicroscopy.github.io/implementati...
August 21, 2025 at 2:22 PM
Diverse approaches exist! The code is often hidden in the suppl. info, so we created an online database, with links to code repos and practical info. We collect 10 implementations of smart microscopy workflows from industry and academia: smartmicroscopy.github.io/implementati...
A hardware agnostic standard for describing acquisition events (e.g. useq-schema) -- think of it like image metadata BEFORE acquiring the image. Microscope control software decides how to execute the acq. event on the hardware (requires support of the microscope control software).
August 21, 2025 at 2:22 PM
A hardware agnostic standard for describing acquisition events (e.g. useq-schema) -- think of it like image metadata BEFORE acquiring the image. Microscope control software decides how to execute the acq. event on the hardware (requires support of the microscope control software).
Device level standardization: when using e.g. micro-manager, every hardware device type uses the same API -- a Nikon stage can be controlled with the same command as a Thorlabs stage (requires availability of drivers, can limit devices to a certain range of functionality).
August 21, 2025 at 2:22 PM
Device level standardization: when using e.g. micro-manager, every hardware device type uses the same API -- a Nikon stage can be controlled with the same command as a Thorlabs stage (requires availability of drivers, can limit devices to a certain range of functionality).
Different strategies are used to run an experiment on different hardware: With an extra software communication layer, one can write adapters for different proprietary software systems (requires effort to write/maintain adapters).
August 21, 2025 at 2:22 PM
Different strategies are used to run an experiment on different hardware: With an extra software communication layer, one can write adapters for different proprietary software systems (requires effort to write/maintain adapters).
Not only acquisition settings can be changed, but also perturbation: Popular is automated targeting of photomanipulation:
August 21, 2025 at 2:22 PM
Not only acquisition settings can be changed, but also perturbation: Popular is automated targeting of photomanipulation:
For example event-driven acquisition: rare events (here mitoses) are detected in a low-res overview scan, the microscope switches objective to automatically image only the mitotic cells in high-res. 🔎
August 21, 2025 at 2:22 PM
For example event-driven acquisition: rare events (here mitoses) are detected in a low-res overview scan, the microscope switches objective to automatically image only the mitotic cells in high-res. 🔎
🔬🧠 Our paper on smart microscopy & the issue of interoperability! www.biorxiv.org/content/10.1... LONG THREAD WARNING: Smart microscopy uses real-time image analysis to automatically guide the acquisition or perturbation of the sample (closed feedback-control loop). Many applications exist:
August 21, 2025 at 2:22 PM
🔬🧠 Our paper on smart microscopy & the issue of interoperability! www.biorxiv.org/content/10.1... LONG THREAD WARNING: Smart microscopy uses real-time image analysis to automatically guide the acquisition or perturbation of the sample (closed feedback-control loop). Many applications exist:
trypanosoma parasites before/after expansion microscopy from neighbor lab. having fun at the institute @izb-unibern.bsky.social ! (btw there is an open assist. prof position - can def. recommend if you enjoy late night recreational microscopy)
August 14, 2025 at 9:11 PM
trypanosoma parasites before/after expansion microscopy from neighbor lab. having fun at the institute @izb-unibern.bsky.social ! (btw there is an open assist. prof position - can def. recommend if you enjoy late night recreational microscopy)
for MCF10A also seems to be dependent a lot on density! looks very different compared to this (over)confluent epithelia i imaged some time ago on confocal. +1 for zarr+dask, has been working great for us with on data 👌 any tricks on how to convert .czi to .zarr without loosing compression?
July 26, 2025 at 3:49 PM
for MCF10A also seems to be dependent a lot on density! looks very different compared to this (over)confluent epithelia i imaged some time ago on confocal. +1 for zarr+dask, has been working great for us with on data 👌 any tricks on how to convert .czi to .zarr without loosing compression?
most expensive office printer 😅
July 26, 2025 at 2:08 PM
most expensive office printer 😅
look how flat they are??? 🥞 nuclear marker is H2B
July 26, 2025 at 8:33 AM
look how flat they are??? 🥞 nuclear marker is H2B