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Reposted by Daniel Krentzel

Jean-Yves Tinevez @jytinevez.bsky.social · 3d

Job alert!

We are looking for a bioimage analysis to work in an image analysis core facility in beautiful Paris. Can I ask you to share this opportunity with your networks?

See also on the forum:
forum.image.sc/t/research-e...

Research engineer in Bioimage Analysis for the researchers of the inIdEx FORMULA

Hi all We are looking for a bioimage analysis to work in an image analysis core facility in beautiful Paris. Can I ask you to share this opportunity with your networks? The position is in the Instit...

forum.image.sc

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Reposted by Daniel Krentzel

Anna Foix @afoix.bsky.social · 17d

Happy to share that ShapeEmbed has been accepted at @neuripsconf.bsky.social 🎉 SE is self-supervised framework to encode 2D contours from microscopy & natural images into a latent representation invariant to translation, scaling, rotation, reflection & point indexing
📄 arxiv.org/pdf/2507.01009 (1/N)

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The Company of Biologists @biologists.bsky.social · 28d

We're excited to announce the first of two prize winners in our #biologists100 #sustainable #travel blog competition. Read Lea’s experience of travelling via four trains from France to Liverpool.

www.biologists.com/stories/my-j...

Stay tuned for next week’s post from winner two.

#Sustainability

My journey from Paris to Liverpool in four trains

8 September 2025 by Léa Manke My journey to the Biologists @ 100 conference began early on Saturday morning. Clutching my thermos filled with coffee, I made my way to the major train station in…

www.biologists.com

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Romain F. Laine @lainebioimaging.bsky.social · 28d

Beautiful work from @danielkrentzel.bsky.social here!

Correlative EM-LM made easy!
Really grateful to be part of the team.

Daniel Krentzel @danielkrentzel.bsky.social · Sep 10

Super happy to see CLEM-Reg out in @natmethods.nature.com! A short thread on the algorithm behind it and how to try it out for yourself🧵(1/9)

www.nature.com/articles/s41...

CLEM-Reg: an automated point cloud-based registration algorithm for volume correlative light and electron microscopy - Nature Methods

CLEM-Reg automates the three-dimensional alignment of volume correlative light and electron microscopy datasets by leveraging probabilistic point cloud registration techniques for fast and accurate re...

www.nature.com

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Daniel Krentzel @danielkrentzel.bsky.social · 28d

Thank you so much for having been part of the journey 🙏

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Nature Methods @natmethods.nature.com · 29d

CLEM-Reg automates the 3D alignment of volume correlative light and electron microscopy data.

www.nature.com/articles/s41...

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Ricardo Henriques @henriqueslab.bsky.social · 29d

Awesome to see this out. Thank you for bringing us in the journey @em-stp.bsky.social and @martinjones.bsky.social. Keep rocking @danielkrentzel.bsky.social!

Daniel Krentzel @danielkrentzel.bsky.social · Sep 10

Super happy to see CLEM-Reg out in @natmethods.nature.com! A short thread on the algorithm behind it and how to try it out for yourself🧵(1/9)

www.nature.com/articles/s41...

CLEM-Reg: an automated point cloud-based registration algorithm for volume correlative light and electron microscopy - Nature Methods

CLEM-Reg automates the three-dimensional alignment of volume correlative light and electron microscopy datasets by leveraging probabilistic point cloud registration techniques for fast and accurate re...

www.nature.com

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Reposted by Daniel Krentzel

Jean-Yves Tinevez @jytinevez.bsky.social · Sep 10

Save the date! The @pasteur.fr Pasteur course on image analysis is announced:

It will happen from the 1st of June to the 5th 2026.

This year there will be only one track: the Early Career Investigator track (beginners). 👇

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Reposted by Daniel Krentzel

Carles Bosch @carlesbosch.bsky.social · Sep 10

#preprint:

We optimised the preparation of tissues for #X-ray phase contrast imaging.

Drying tissue samples (instead of embedding them) brings more signal in #X-ray phase contrast images.

The process largely preserves #ultrastructure.

@safekhan.bsky.social @andreas-t-schaefer.bsky.social

Safe Khan @safekhan.bsky.social · Sep 10

Our pre-print is out!
Critical point drying of brain tissue for x-ray phase contrast imaging.
@apeart.bsky.social @yuxinzhang.bsky.social @jkbrmn.bsky.social @apacureanu.bsky.social @andreas-t-schaefer.bsky.social
@carlesbosch.bsky.social
@esrf.fr
@crick.ac.uk
bioarXiv: doi.org/10.1101/2025...

Critical point drying of brain tissue for X-ray phase contrast imaging

X-ray phase contrast tomography is emerging as a powerful method for imaging large volumes of brain tissue at sub-cellular resolution. However, current sample preparation methods are largely inherited...

doi.org

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Daniel Krentzel @danielkrentzel.bsky.social · Sep 10

Thank you!

Daniel Krentzel @danielkrentzel.bsky.social · Sep 10

Finally, I want to give a massive thanks to the amazing team behind CLEM-Reg 🙏

@matous-elphick.bsky.social, @lainebioimaging.bsky.social @henriqueslab.bsky.social, @em-stp.bsky.social, @martinjones.bsky.social, MC, Chris and Cameron

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Daniel Krentzel @danielkrentzel.bsky.social · Sep 10

The plugin can also be run in separate steps for debugging and to use different segmentation algorithms for registration. (9/9)

www.youtube.com/watch?v=cypD...

CLEM-Reg Split Registration Tutorial

YouTube video by dkrentzel

www.youtube.com

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Daniel Krentzel @danielkrentzel.bsky.social · Sep 10

💻 You can directly try out CLEM-Reg for yourself with our @napari.org plugin where we also include a sample benchmark dataset.

Installation instructions are here 👉 github.com/krentzd/napa... (8/9)

www.youtube.com/watch?v=ud3z...

CLEM-Reg Tutorial

YouTube video by dkrentzel

www.youtube.com

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Daniel Krentzel @danielkrentzel.bsky.social · Sep 10

📊🎯 We evaluated the performance of CLEM-Reg against an expert electron microscopist using lysosomes as target structures and found that CLEM-Reg aligns lysosomes with submicron accuracy (7/9)

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Daniel Krentzel @danielkrentzel.bsky.social · Sep 10

3️⃣ Finallly, the fluorescence image is overlaid to the electron microscopy image with the transform found from the point cloud registration. (6/9)

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Daniel Krentzel @danielkrentzel.bsky.social · Sep 10

2️⃣ Then, we sample point clouds from the segmentations to obtain a modality-agnostic and lightweight representation. The two resulting point clouds are then registered using a probabilistic point cloud registration algorithm. (5/9)

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Daniel Krentzel @danielkrentzel.bsky.social · Sep 10

1️⃣ CLEM-Reg starts off by segmenting mitochondria in both the fluorescence and the electron microscopy images. Mitochondria work well, because they're usually very well distributed across the cell. (4/9)

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Daniel Krentzel @danielkrentzel.bsky.social · Sep 10

And this is why we developed CLEM-Reg, an algorithm that automatically and accurately registers vCLEM images in minutes. (3/9)

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Daniel Krentzel @danielkrentzel.bsky.social · Sep 10

For most image registration tasks, intensity-based methods work well. Correlative light and electron microscopy data are, however, a lot trickier to align, because of the massive differences in visual appearance. As a result, CLEM data is usually registered manually. (2/9)

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Daniel Krentzel @danielkrentzel.bsky.social · Sep 10

Super happy to see CLEM-Reg out in @natmethods.nature.com! A short thread on the algorithm behind it and how to try it out for yourself🧵(1/9)

www.nature.com/articles/s41...

CLEM-Reg: an automated point cloud-based registration algorithm for volume correlative light and electron microscopy - Nature Methods

CLEM-Reg automates the three-dimensional alignment of volume correlative light and electron microscopy datasets by leveraging probabilistic point cloud registration techniques for fast and accurate re...

www.nature.com

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Reposted by Daniel Krentzel

Institut Pasteur | 130 years of biomedical research @pasteur.fr · Sep 1

🎓 Applications for Institut Pasteur's PhD programs open Sept 1-Oct 20, 2025 for October 2026 entry.

Apply to up to 4 projects across 6 programs: PPU, PPU-IMAGINE @institutimagine.bsky.social, [email protected], PPU-EID @upcite.bsky.social & more 🧬

Register now ✍️ www.pasteur.fr/en/education...

Pasteur-Paris University International Doctoral Programme, The call for enrollment of students in October 2026 will be open from September 1st to October 20th, 2025

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Reposted by Daniel Krentzel

Ricardo Henriques @henriqueslab.bsky.social · Jul 10

🚨Join us! We're soon opening 3 postdoctoral positions in #AIDrivenBiology. Seeking biologists (especially microbiology and infection biology), computer scientists, and microscopy developers. Ideal candidates are those eager to use or develop next-gen tech for cell biology. Get in touch (DM/email)

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Martin Weigert @maweigert.bsky.social · Jul 10

Do you like developing new AI vision methods for microscopy image analysis? You love theory & implementation? 1 week left to apply for a fully funded PhD position in our lab in Dresden 🇩🇪! Topics: object detection/tracking, multimodal models & more. DM/email for details! #PhD #AcademicJobs #GPUsgoBrr

Vacancy ID 12244

www.verw.tu-dresden.de

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Tom Cumming @tomcumming.bsky.social · May 21

The effector caspases drive cell death, but their activation can often be survived, so how do cells make this decision? Our new preprint from @levayerr.bsky.social shows that instantaneous caspase activity is important, but past activation has a key role to play!

www.biorxiv.org/content/10.1...

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Levayer Lab @levayerr.bsky.social · May 21

Many cells during development are exposed to caspase activation and yet survive. Why some die and not others ? We found out that the memory of previous caspase activation bias significantly later death comitment and bias death distribution and single cell decision
www.biorxiv.org/content/10.1...

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