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Reposted by Martin Jones

Jean-Yves Tinevez @jytinevez.bsky.social · 2d

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 Martin Jones

Reto Fiolka @retof.bsky.social · 3d

We present multi-immersion Oblique Plane microscope (miOPM), a light-sheet platform that can be adapted to a wide range of applications, from sensitive live cell imaging to imaging organs and cleared tissues.
www.biorxiv.org/content/10.1...

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Reposted by Martin Jones

David Legland @dlegland.bsky.social · 10d

Thrilled to share that our article in @jofmicroscopy.bsky.social is now accessible online and as open access! If you wonder how to start the analysis of your images, we propose a decision tree to help identify suitable methods. Just follow the link(s)...

#imageanalysis #bioimaging

jofmicroscopy.bsky.social @jofmicroscopy.bsky.social · 10d

"From cells to pixels: A decision tree for designing bioimage analysis pipelines" by Elnaz Fazeli, Robert Haase, Michael Doube, Kota Miura & David Legland is free-to-view here: doi.org/10.1111/jmi....

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Reposted by Martin Jones

Dave Barry @david-j-barry.bsky.social · 6d

I forgot that I had this made. As a prototype that never went into full production, it's the only one in existence and, therefore, highly desirable.

Let's start the bidding at £1,809, £1 for every day since the very first CBIAS.

For an extra 50%, you can have it signed by @martinjones.bsky.social.

Crick BioImage Analysis Symposium 2024 Commemorative Mug

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Reposted by Martin Jones

The BioImage Archive @bioimagearchive.bsky.social · 24d

🎉 Our paper “MIFA: Metadata, Incentives, Formats and Accessibility guidelines to improve the reuse of AI datasets for bioimage analysis” is out in @natmethods.nature.com!
Community-driven standards to make bioimage data AI-ready & reusable.
👉 www.nature.com/articles/s41... #AI #Bioimaging #FAIRdata

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Reposted by Martin Jones

BioImaging North America @bioimagingna.bsky.social · 27d

#HappyFluorescenceFriday!

#microscopycommunity-new to the field of bioimaging or just looking to brush up? Wed Sept 17, the I&E tools series will bring a talk on raw image data- don’t miss out on setting yourself up for success- join us!

More info: buff.ly/BIhYKtO

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Reposted by Martin Jones

Florian Jug @florianjug.bsky.social · 27d

🚨 Wow, that really sounds like an amazing opportunity… If I were a bit younger, I would start preparing my application already… 😮

www.scilifelab.se/news/ready-t...

Ready to shape the future of AI in life science?

The next call for DDLS Fellows is opening soon, offering an outstanding opportunity for ambitious young researchers to establish their own internationally competitive research groups. This round has a...

www.scilifelab.se

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Reposted by Martin Jones

The Francis Crick Institute @crick.ac.uk · 27d

Want to enhance your image analysis skills with napari?

We’re running a two-day training event on how to use napari to effectively analyse your bioimaging data.

🕒 Applications close on 15 September.

Learn more and apply 👇

www.crick.ac.uk/whats-on/cbi...

CBIAS napari workshop 2025

www.crick.ac.uk

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Reposted by Martin Jones

Nature Methods @natmethods.nature.com · 28d

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

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

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Reposted by Martin Jones

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 · 29d

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 Martin Jones

Daniel Krentzel @danielkrentzel.bsky.social · 29d

💻 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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Reposted by Martin Jones

Daniel Krentzel @danielkrentzel.bsky.social · 29d

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 Martin Jones

FocalPlane @focalplane.bsky.social · Sep 3

📢Introducing Microscopy New Zealand 🔬

Alfonso Schmidt @malaghan.bsky.social, current MNZ president, shares the history of MNZ, its objectives and the society’s latest activities.

An introduction to Microscopy New Zealand - FocalPlane

An introduction to Microscopy New Zealand - News

focalplane.biologists.com

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Reposted by Martin Jones

Joel Lüthi @joelluethi.bsky.social · Aug 25

We're happy to announce the 2025 International OME-NGFF workshop 🎉

📅 Dates:
- Symposium: Nov 10–11, 2025
- Hackathon: Nov 12–14, 2025

📍 Location: Zurich, Switzerland

Full details & registration: www.biovisioncenter.uzh.ch/en/events/Up...

#bioimaging #openscience #OMENGFF #OMEZarr

(1/x 🧵)

Visual of segmented human induced pluripotent stem cells with the key workshop dates: Symposium on November 10-11, Hackathon on November 12-14th in Zurich Switzerland

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Reposted by Martin Jones

Kyle Harrington @kyleharrington.com · Aug 26

Better ML for cryo-ET starts with better benchmarks.

We built a phantom cryo-ET dataset (~500 tomograms) + hosted a Kaggle challenge.

The result: community models beat expert tools.

Read more in the @natmethods.nature.com article that just came out:
🔗 doi.org/10.1038/s415...

A realistic phantom dataset for benchmarking cryo-ET data annotation - Nature Methods

A standardized, realistic phantom dataset consisting of ground-truth annotations for six diverse molecular species is provided as a community resource for cryo-electron-tomography algorithm benchmarki...

doi.org

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Reposted by Martin Jones

EMBL-EBI @ebi.embl.org · Aug 27

Meet Aybuke Kupcu Yoldas 🇹🇷🇬🇧 our BioImage Archive Data Project Leader.

Aybuke swapped telescopes for microscopes and stars ⭐ for cells a few years ago, when she pivoted from astrophysics to bioimaging.

She now helps make bioimages easy to access and reuse.

www.ebi.ac.uk/about/news/p...

We are EMBL: Aybuke Kupcu Yoldas on trading stars for cells

Aybuke Kupcu Yoldas, Senior Imaging Bioinformatician at EMBL-EBI, talks about the Bioimage Archive and her journey from astrophysics to biology

www.ebi.ac.uk

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Reposted by Martin Jones

Crick BioImage Analysis Symposium @cbias.bsky.social · Aug 20

The line-up for guest speakers at #CBIAS2025 is looking great! 🎉

We'll introduce them to you in the coming days, on the lead up to the deadline for abstract submission on August 31st.

If you want a sneak peek in the meantime, check our website!
www.crick.ac.uk/whats-on/cri...

Crick BioImage Analysis Symposium 2025

www.crick.ac.uk

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Reposted by Martin Jones

Crick BioImage Analysis Symposium @cbias.bsky.social · Aug 21

Our first #CBIAS2025 invited speaker is Andrew French from @uniofnottingham.bsky.social‬, who specialises in using AI to understand images. Their research interests include image analysis of plants and complex structures and image capture automation

🔗👇
www.nottingham.ac.uk/biosciences/...

People - The University of Nottingham

www.nottingham.ac.uk

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Reposted by Martin Jones

Hannah Heil @hannah-superres.bsky.social · Aug 20

🚨 New preprint on bioRxiv! 🚨
Smart microscopy🔬 is reshaping life sciences—but progress is slowed by fragmentation.
@lhinderling.bsky.social & the Smart Microsopy Working Group maps the field & proposes a path toward an open, interoperable future.
🧵👇
doi.org/10.1101/2025...

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Reposted by Martin Jones

Dave Barry @david-j-barry.bsky.social · Aug 20

ONLY 11 MORE DAYS TO SUBMIT AN ABSTRACT FOR #CBIAS2025!!!

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Reposted by Martin Jones

Crick BioImage Analysis Symposium @cbias.bsky.social · Aug 8

Abstract submission #CBIAS2025 is closing on August 31st - we invite submissions on all topics related to #bioimageanalysis: new tools, biological discoveries using existing methods, and anything in between. Early-career researchers especially encouraged to submit!

www.crick.ac.uk/whats-on/cri...

Crick BioImage Analysis Symposium 2025

www.crick.ac.uk

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Reposted by Martin Jones

Crick BioImage Analysis Symposium @cbias.bsky.social · Aug 11

📢 After #CBIAS2025, join our hands-on 2-day napari training by @crick.ac.uk @ucl.ac.uk @liverpooluni.bsky.social
From conda to plugins to Jupyter, practicals on real data with expert guidance.
For Python/ImageJ coders. Apply by 1 Sept – limited to 30! crick.ac.uk/whats-on/cbias-napari-workshop-2025

CBIAS napari workshop 2025

crick.ac.uk

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Reposted by Martin Jones

Chris Lintott @chrislintott.bsky.social · Aug 15

This is really lovely. (Though I'm not sure the note about Nobelists quite translates to physics/astro).

Richard Sever @richardsever.bsky.social · Aug 15

"why [would] anyone intelligent enough to be a scientist choose to be one [given] the unfavorable risk-to-reward ratio "?

One of the most intelligent people you could meet offers some answers: having ideas, watching them develop, and sharing them journals.biologists.com/jcs/article/...

Why would anyone want to be a scientist?

It is difficult to fathom why anyone intelligent enough to be a scientist would actually choose to be one. Doing good science requires the utmost exertion of body, mind and spirit, yet is consistently...

journals.biologists.com

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Reposted by Martin Jones

EMBL Events @events.embl.org · Aug 14

🔬 Do you want to learn the state-of-the-art SEM-based volume EM techniques and gain practical knowledge in imaging and data processing? Then don't miss the chance to apply for #EMBOvEM!

Apply by 31 August 👉 https://s.embl.org/vem25-01-bl

🗓️ 23 – 28 November 2025
📍 EMBL Heidelberg

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Reposted by Martin Jones

OME @openmicroscopy.org · Aug 6

New Imaging Mass Cytometry data in the Image Data Resource (IDR, idr.openmicroscopy.org).

IDR: Image Data Resource

idr.openmicroscopy.org

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