Daniel Krentzel
@danielkrentzel.bsky.social
Hunting for new antibiotics with deep learning at @pasteur.fr 🧫 | Previously @crick.ac.uk and 🎓 @imperialcollegeldn.bsky.social
Pinned
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
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...
www.nature.com/articles/s41...
Reposted by Daniel Krentzel
We had an amazing OME-NGFF hackathon last week, Wednesday to Friday, following the inspiring OME-NGFF symposium. What a fantastic week! It’s hard to describe how motivating it is to be surrounded by so many talented, curious & friendly people who care deeply about open, FAIR bioimaging data.
1/14 🧵
1/14 🧵
November 17, 2025 at 1:24 PM
We had an amazing OME-NGFF hackathon last week, Wednesday to Friday, following the inspiring OME-NGFF symposium. What a fantastic week! It’s hard to describe how motivating it is to be surrounded by so many talented, curious & friendly people who care deeply about open, FAIR bioimaging data.
1/14 🧵
1/14 🧵
Reposted by Daniel Krentzel
A great plugin prototype to run Fractal tasks interactively in napari: Making interoperable workflow tasks accessible directly in a viewer
(8/14 🧵)
(8/14 🧵)
November 17, 2025 at 1:24 PM
A great plugin prototype to run Fractal tasks interactively in napari: Making interoperable workflow tasks accessible directly in a viewer
(8/14 🧵)
(8/14 🧵)
If you're interested in developing an open-source image analysis platform/plugin to profile bacteria with deep learning while living in the beautiful city of Paris 🇫🇷, check out this job ad from the @chzimmer.bsky.social lab @pasteur.fr
research.pasteur.fr/fr/job/open-...
research.pasteur.fr/fr/job/open-...
Open-Source Developer for Deep Learning Antibiotic Discovery Platform - Research
Introduction Antimicrobial resistance (AMR) is one of the most urgent global health threats projected to cause up to 10 million deaths per year by 2050. The AI4AMR project brings together teams from I...
research.pasteur.fr
November 15, 2025 at 9:22 AM
If you're interested in developing an open-source image analysis platform/plugin to profile bacteria with deep learning while living in the beautiful city of Paris 🇫🇷, check out this job ad from the @chzimmer.bsky.social lab @pasteur.fr
research.pasteur.fr/fr/job/open-...
research.pasteur.fr/fr/job/open-...
Reposted by Daniel Krentzel
In vivo antimicrobial activity of engineered mesoporous silica nanoparticles targeting intracellular #mycobacteria
(doxycycline-loaded nanoparticles, zebrafish model of Mycobacterium marinum #infection)
@lkremer1.bsky.social
#DrugDevelopment
(doxycycline-loaded nanoparticles, zebrafish model of Mycobacterium marinum #infection)
@lkremer1.bsky.social
#DrugDevelopment
In vivo antimicrobial activity of engineered mesoporous silica nanoparticles targeting intracellular mycobacteria - Nature Communications
Current treatment options for Mycobacterium marinum infections are extensive and challenging. In this work, authors explore the potential of functionalized mesoporous silica nanoparticles as a carrier for delivery of drugs against M. marinum.
bit.ly
October 16, 2025 at 9:29 AM
In vivo antimicrobial activity of engineered mesoporous silica nanoparticles targeting intracellular #mycobacteria
(doxycycline-loaded nanoparticles, zebrafish model of Mycobacterium marinum #infection)
@lkremer1.bsky.social
#DrugDevelopment
(doxycycline-loaded nanoparticles, zebrafish model of Mycobacterium marinum #infection)
@lkremer1.bsky.social
#DrugDevelopment
Reposted by Daniel Krentzel
** 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.
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.
October 5, 2025 at 9:48 PM
** 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.
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.
Reposted by Daniel Krentzel
🚨 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
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
October 13, 2025 at 11:58 AM
🚨 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
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
Reposted by Daniel Krentzel
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...
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
October 7, 2025 at 12:39 PM
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...
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...
Reposted by Daniel Krentzel
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)
📄 arxiv.org/pdf/2507.01009 (1/N)
September 23, 2025 at 8:32 AM
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)
📄 arxiv.org/pdf/2507.01009 (1/N)
Reposted by Daniel Krentzel
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
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
September 12, 2025 at 11:45 AM
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
www.biologists.com/stories/my-j...
Stay tuned for next week’s post from winner two.
#Sustainability
Reposted by Daniel Krentzel
Beautiful work from @danielkrentzel.bsky.social here!
Correlative EM-LM made easy!
Really grateful to be part of the team.
Correlative EM-LM made easy!
Really grateful to be part of the team.
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...
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
September 11, 2025 at 4:21 PM
Beautiful work from @danielkrentzel.bsky.social here!
Correlative EM-LM made easy!
Really grateful to be part of the team.
Correlative EM-LM made easy!
Really grateful to be part of the team.
Reposted by Daniel Krentzel
CLEM-Reg automates the 3D alignment of volume correlative light and electron microscopy data.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
September 11, 2025 at 2:25 PM
CLEM-Reg automates the 3D alignment of volume correlative light and electron microscopy data.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Daniel Krentzel
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!
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...
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
September 10, 2025 at 7:09 PM
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!
Reposted by Daniel Krentzel
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). 👇
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). 👇
September 10, 2025 at 12:50 PM
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). 👇
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). 👇
Reposted by Daniel Krentzel
#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
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
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.
@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
September 10, 2025 at 3:51 PM
#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
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
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...
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
September 10, 2025 at 9:37 AM
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...
www.nature.com/articles/s41...
Reposted by Daniel Krentzel
🎓 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...
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...
September 1, 2025 at 9:44 AM
🎓 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...
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...
Reposted by Daniel Krentzel
🚨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)
July 10, 2025 at 8:34 AM
🚨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)
Reposted by Daniel Krentzel
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
July 10, 2025 at 1:49 PM
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
Reposted by Daniel Krentzel
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...
www.biorxiv.org/content/10.1...
May 21, 2025 at 8:52 AM
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...
www.biorxiv.org/content/10.1...
Reposted by Daniel Krentzel
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...
www.biorxiv.org/content/10.1...
May 21, 2025 at 9:40 AM
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...
www.biorxiv.org/content/10.1...
Reposted by Daniel Krentzel
Researchers paid $9 billion over 5 years for their findings to be freely accessible.
This is based on a study of the global expenditure on article processing charges (APCs) paid to six publishers for open access between 2019 and 2023. arxiv.org/abs/2407.16551
This is based on a study of the global expenditure on article processing charges (APCs) paid to six publishers for open access between 2019 and 2023. arxiv.org/abs/2407.16551
Estimating global article processing charges paid to six publishers for open access between 2019 and 2023
This study presents estimates of the global expenditure on article processing charges (APCs) paid to six publishers for open access between 2019 and 2023. APCs are fees charged for publishing in some ...
arxiv.org
January 26, 2025 at 5:12 PM
Researchers paid $9 billion over 5 years for their findings to be freely accessible.
This is based on a study of the global expenditure on article processing charges (APCs) paid to six publishers for open access between 2019 and 2023. arxiv.org/abs/2407.16551
This is based on a study of the global expenditure on article processing charges (APCs) paid to six publishers for open access between 2019 and 2023. arxiv.org/abs/2407.16551
Reposted by Daniel Krentzel
I will be recruiting new postdocs with start dates end 2025 - early 2026. If you'd like to work at the Pasteur Institute in the heart of Paris surrounded by amazing scientists, reach out to discuss possible projects on SynBio / Bacterial Immunity!
May 18, 2025 at 3:20 PM
I will be recruiting new postdocs with start dates end 2025 - early 2026. If you'd like to work at the Pasteur Institute in the heart of Paris surrounded by amazing scientists, reach out to discuss possible projects on SynBio / Bacterial Immunity!
Reposted by Daniel Krentzel
Day 4, with @jytinevez.bsky.social and tracking! #neubiaspasteur2025
May 15, 2025 at 3:01 PM
Day 4, with @jytinevez.bsky.social and tracking! #neubiaspasteur2025
Reposted by Daniel Krentzel
4th day on the go for #neubiaspasteur2025 with a @biapyx.bsky.social practical course by @jwpylvanainen.bsky.social and a #cellpose #dask and RNA2Seg (doi.org/10.1101/2025...) course with @gaellel.bsky.social and Alice Blondel
May 15, 2025 at 12:33 PM
4th day on the go for #neubiaspasteur2025 with a @biapyx.bsky.social practical course by @jwpylvanainen.bsky.social and a #cellpose #dask and RNA2Seg (doi.org/10.1101/2025...) course with @gaellel.bsky.social and Alice Blondel
Reposted by Daniel Krentzel
3rd day of the #NEUBIASpasteur2025 with a introduction lecture to OMICS by Florian Muller, followed by a full day of #qupath by Thierry Pecot and #ome-zarr / #dask by @m-albert.bsky.social
May 14, 2025 at 10:22 AM
3rd day of the #NEUBIASpasteur2025 with a introduction lecture to OMICS by Florian Muller, followed by a full day of #qupath by Thierry Pecot and #ome-zarr / #dask by @m-albert.bsky.social