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Reposted by Daniel Krentzel

Christophe Zimmer @chzimmer.bsky.social · 9d

** Now seeking postdocs **

Join our interdisciplinary and transnational team in Würzburg (Germany) or Paris (France) to drive projects in translational biology and antibiotic drug discovery.
Backgrounds in computational biology, AI, physics, or microbiology are all welcome. Please spread the word.

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Institut Pasteur Education @pasteuredu.bsky.social · 1d

🚨 1 week left to apply for the Pasteur-Paris University International PhD Program (PPU)!

Join an international community of scientists at the Institut Pasteur 🌍 Dedicated support, mentorship & world-class labs included.

📅Deadline: Oct 20, 2025
🎓Program start: October 2026

👉 Apply: bit.ly/CallPPU

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Jean-Yves Tinevez @jytinevez.bsky.social · 7d

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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Anna Foix @afoix.bsky.social · 21d

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 · Sep 12

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 · Sep 11

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 · Sep 11

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

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Nature Methods @natmethods.nature.com · Sep 11

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 · Sep 10

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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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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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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