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Ignacio Arganda-Carreras @iarganda.bsky.social · 7h

✨ Fantastic opportunity for people looking for image facility jobs! What better than working with the awesome @jytinevez.bsky.social in Paris? 🤩

#bioimaging #bioimageanalysis #facilityjob

👇

Jean-Yves Tinevez @jytinevez.bsky.social · 1d

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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Ignacio Arganda-Carreras @iarganda.bsky.social · 1d

👇 The official call opening has been delayed ⌛ by the university to the end of this week.

Sorry about that, I'll keep you posted! 🙏

Ignacio Arganda-Carreras @iarganda.bsky.social · 8d

📣 We’re hiring, please RT! Fully funded 4-year PhD position in our CVPD group at @informatikaehu.bsky.social!

Research at the intersection of AI, deep learning & bioimage analysis. 🧠🔬

📅 Applications open Oct 6 (deadline: ~Oct 27)
📍 San Sebastian, Spain.
👉 cvpd.github.io/post/2025-09...

📢 Open 4-year PhD Position in Deep Learning for Bioimage Analysis! | CVPD Research group

The Computer Vision and Pattern Discovery (CVPD) group at the University of the Basque Country (UPV/EHU) is offering a fully funded 4-year PhD position within the recently awarded project TOSBI: Towar...

cvpd.github.io

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Ignacio Arganda-Carreras @iarganda.bsky.social · 5d

#skyvision 🤓🤗

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Ignacio Arganda-Carreras @iarganda.bsky.social · 5d

In case someone prefers to apply this way, I also opened a LinkedIn job offer:

www.linkedin.com/jobs/view/43...

#phd #bioimaging #deeplearning #bioimageanalysis #joboffer

EHU hiring 4-year PhD Position in Deep Learning for Bioimage Analysis in San Sebastián, Basque Country, Spain | LinkedIn

Posted 8:40:15 AM. The Computer Vision and Pattern Discovery (CVPD) group at the University of the Basque Country…See this and similar jobs on LinkedIn.

www.linkedin.com

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Ignacio Arganda-Carreras @iarganda.bsky.social · 7d

Thanks a lot, @lmescu.bsky.social ! 🤗

1

Ignacio Arganda-Carreras @iarganda.bsky.social · 7d

🥲

Ignacio Arganda-Carreras @iarganda.bsky.social · 8d

📣 We’re hiring, please RT! Fully funded 4-year PhD position in our CVPD group at @informatikaehu.bsky.social!

Research at the intersection of AI, deep learning & bioimage analysis. 🧠🔬

📅 Applications open Oct 6 (deadline: ~Oct 27)
📍 San Sebastian, Spain.
👉 cvpd.github.io/post/2025-09...

📢 Open 4-year PhD Position in Deep Learning for Bioimage Analysis! | CVPD Research group

The Computer Vision and Pattern Discovery (CVPD) group at the University of the Basque Country (UPV/EHU) is offering a fully funded 4-year PhD position within the recently awarded project TOSBI: Towar...

cvpd.github.io

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Reposted by Ignacio Arganda-Carreras

Katedra @katedra.eus · 18d

Resulta que en #NaukasBilbao25 hasta las moléculas de agua bailan, con @elirezabal.bsky.social

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Ignacio Arganda-Carreras @iarganda.bsky.social · 18d

Online aquí: naukas.com/2025/09/19/s...

Sigue en directo Naukas Bilbao 15º Aniversario - Naukas

Edición especial 15º Aniversario – Palacio Euskalduna de Bilbao – Viernes 19 y sábado 20 de septiembre. En colaboración con la Cátedra de Cultura Científica de la UPV/EHU hemos preparado un fantástico...

naukas.com

Ignacio Arganda-Carreras @iarganda.bsky.social · 18d

¿Alguien en Bilbao hoy (sábado 20 de septiembre)?

No perderse la charla de la maravillosa @elirezabal.bsky.social 😍 (@theochemehu.bsky.social, @dipcehu.bsky.social) en @naukas.bsky.social #NAUKAS2025

⏰11:30 a 11:40 – 💫Elixabete Rezabal💫 – ¿Hueles vibraciones? 👃📳

naukas.com/2025/09/12/p...

Programa definitivo de Naukas Bilbao 15º Aniversario - Naukas

Programa definitivo Naukas Bilbao 15 Aniversario (19 al 21 septiembre 2025)

naukas.com

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Reposted by Ignacio Arganda-Carreras

Nick Lloyd @spaincivilwartours.bsky.social · 18d

First page of 18th century Basque-Icelandic dictionary. A Basque-Icelandic pidgin was spoken between locals and Basque whalers from ~1600 including the well-known expression "Fenicha for ju" meaning F**k you! en.m.wikipedia.org/wiki/Basque%...

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Ignacio Arganda-Carreras @iarganda.bsky.social · 18d

Oh là là 😍

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Ignacio Arganda-Carreras @iarganda.bsky.social · 19d

And that’s a wrap! I’m flying home. Hope everybody had as much fun as I had 🤗

@ahklemm.bsky.social @perrinegil.bsky.social @tischi.bsky.social you’re awesome!

Big thanks to all speakers & students & @events.embl.org staff for this amazing week 🤩

a cartoon llama is holding a microphone and the words boom are above it

ALT: a cartoon llama is holding a microphone and the words boom are above it

media.tenor.com

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Ignacio Arganda-Carreras @iarganda.bsky.social · 19d

Last but not least, we have @philippeandrey.bsky.social from @inrae-france.bsky.social with Practical session 7: "Statistical spatial analysis and modeling with BIP" 📊

We're learning about 💫BIP (Biological Image Processing)💫, the command-line 🖥️ #BioimageAnalysis solution from his lab.

Webcam view of the classroom of the EMBO course on "Advanced methods in bioimage analysis", during Practical session 7: "Statistical spatial analysis and modeling with BIP", by Philippe Andrey (Inrae, France).

Zoom view of the screen of Philippe Andrey (Inrae, France) during Practical session 7: "Statistical spatial analysis and modeling with BIP", at of the EMBO course on "Advanced methods in bioimage analysis". The online participant cameras are shown on top, while a Linux terminal with BIP commands is shown on the bottom.

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Ignacio Arganda-Carreras @iarganda.bsky.social · 19d

... domain adaptation🔃, enhancers✨... How cool is that? 😎

Fynn Beuttenmüller is taking to the students during Practical session 6: "AI for Life Sciences", of the EMBO course on Advanced methods in bioimage analysis at EMBL (Heidelberg, Germany). The screen shows the Ilastik interface displaying an EM section with mitochondria segmented in yellow by a domain-adapted model.

Fynn Beuttenmüller is looking at his screen during Practical session 6: "AI for Life Sciences", of the EMBO course on Advanced methods in bioimage analysis at EMBL (Heidelberg, Germany). The screen shows the Ilastik interface displaying an EM section with mitochondria segmented in red by a model enhancer.

Panoramic view of the classroom during Practical session 6: "AI for Life Sciences", of the EMBO course on Advanced methods in bioimage analysis at EMBL (Heidelberg, Germany).

Fynn Beuttenmüller is taking to the students during the exercises of Practical session 6: "AI for Life Sciences", of the EMBO course on Advanced methods in bioimage analysis at EMBL (Heidelberg, Germany).

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Ignacio Arganda-Carreras @iarganda.bsky.social · 19d

Thanks a lot, @ahklemm.bsky.social! It's tough to post on social networks while presenting 😜

I hope the students of the @embo.org course on Advanced methods in #BioimageAnalysis liked @biapyx.bsky.social 🤗

Anna Klemm @ahklemm.bsky.social · 19d

@iarganda.bsky.social also on the stage by himself, giving an introduction to BiaPy @biapyx.bsky.social for streamlining deep-learning workflows. A tool tailored to be convenient to use by the full range of bioimage analysis experts.

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Ignacio Arganda-Carreras @iarganda.bsky.social · 19d

And now Fynn Beuttenmüller from @embl.org is showing us all the cool stuff behind the BioImage Model Zoo 🦒 and @ilastik-team.bsky.social 🖥️🎨

For instance, students learnt how to load and apply the @biapyx.bsky.social models from the zoo into @ilastik-team.bsky.social 😊 ...

Fynn Beuttenmüller addresses the students in the classroom during Practical session 6: "AI for Life Sciences", of the EMBO course on Advanced methods in bioimage analysis at EMBL (Heidelberg, Germany).

Screenshot of the screen during Practical session 6: "AI for Life Sciences", of the EMBO course on Advanced methods in bioimage analysis at EMBL (Heidelberg, Germany). The screen shows the Ilastik interface displaying an EM section with mitochondria segmented in yellow by the model trained previously in BiaPy.

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Ignacio Arganda-Carreras @iarganda.bsky.social · 19d

First part of the session was dedicated to @biapyx.bsky.social, learning 🎓 about how to create #DeepLearning based workflows for #BioimageAnalysis tasks 🛠️

In particular, students got their hands on the notebook 📓 for 2D semantic segmentation:

colab.research.google.com/github/BiaPy...

Google Colab

colab.research.google.com

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Ignacio Arganda-Carreras @iarganda.bsky.social · 19d

And here we are on Day 6️⃣ of our @embo.org course on "Advanced methods in bioimage analysis"! 🔬🖥️📊 @events.embl.org

Anna Kreshuk is already shining at the stage answering questions about Practical session 6: "AI for Life Sciences" 🤖🧬🧪, especially about @ilastik-team.bsky.social ✊🖌️

Classroom view of the Practical session 6: "AI for Life Sciences", on Day 6 of EMBO course on Advanced methods in bioimage analysis. Anna Kreshuk is already addressing the crowd of students, while they seat on their computer posts.

Classroom view of the Practical session 6: "AI for Life Sciences", on Day 6 of EMBO course on Advanced methods in bioimage analysis. Anna Kreshuk answers the questions of the students, while she holds a cup of tea.

Panoramic view of the classroom during Practical session 6: "AI for Life Sciences", on Day 6 of EMBO course on Advanced methods in bioimage analysis. Anna Kreshuk answers the questions of the students from the stage.

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Ignacio Arganda-Carreras @iarganda.bsky.social · 19d

Good night!

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Ignacio Arganda-Carreras @iarganda.bsky.social · 19d

After an intense week of learning, coding and playing with advanced methods on #BioimageAnalysis, a well deserved BBQ 🔥 to recover our strength 💪 for tomorrow, the last day of the course 😢

Enjoy!

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Ignacio Arganda-Carreras @iarganda.bsky.social · 20d

The rest of the afternoon is spent with the students working on their own data with all Software representatives and instructors, of course 🤗

They work that hard, not posing at all! 😆

@jytinevez.bsky.social @perrinegil.bsky.social keep all the attention 😎

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Ignacio Arganda-Carreras @iarganda.bsky.social · 20d

After lunch 🍽️, we go back to work 🛠️ with Lecture 7: "Scientific AI and the future of OME-Zarr" by Matthew McCormick from @fideus-labs.bsky.social, USA.

We're learning about ngff-zarr and getting our hands on converting bioimages to OME-Zarr ✨

Christian Tischer is presenting Matthew McCormick from fideus labs (USA), who will talk online about "Scientific AI and the future of OME-Zarr" (presentation on screen).

Close look at the screens of our 2025 EMBO course. On the left one, we can see the online participants on Zoom, while on the right one we see the presentation by Matthew McCormick from fideus labs (USA), who's presenting a slide that reads "What can ngff-zarr do for you?".

General view of the classroom looking at the online presentation of Matthew McCormick from fideus labs (USA).

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Ignacio Arganda-Carreras @iarganda.bsky.social · 20d

The final lecture of the morning (Lecture 6: Open science and bioimage analysis) is given online by the great @paveltomancak.bsky.social.

We're going through the history of #Fiji and #ImageJ and the big plan behind to Pavel's current projects 🤩

Panoramic view of the classroom waiting for Lecture 6 (Open science and bioimage analysis), while Pavel Tomancak is on screen and Anna Klemm and Christian Tischer are on site organizing the class.

View of the classroom waiting for Lecture 6 (Open science and bioimage analysis) to start, with Pavel Tomancak online.

View of the classroom during Lecture 6 (Open science and bioimage analysis) by Pavel Tomancak online. The screen shows Fiji main plugins and update system.

View of the screens during Lecture 6 (Open science and bioimage analysis) by Pavel Tomancak where we can see "The BIG plan (2007)", with a diagram that goes from Registration to Tracking & Analysis. 2007 and modern pictures of Stephan Preibisch and Stephan Saalfeld are also displayed.

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Ignacio Arganda-Carreras @iarganda.bsky.social · 20d

Without a pause, we (literally) run 🏃 into Lecture 5: "Visualization, annotation and data sharing of large images" with @webknossos.org by @normanrz.com

Discovering the super cool features of WEBKNOSSOS 😮 to deal with the increasing size of #BioimageAnalysis datasets.

Norman Rzepka from Scalable Minds (Germany) about to start his presentation in the EMBO course on Advanced methods in Bioimage Analysis (EMBL, September 2025). The first slide of his presentation reads "WEBKNOSSOS Visualization, annotation and data sharing of large images".

Panoramic view of the classroom before Norman Rzepka from Scalable Minds (Germany) starts his presentation in the EMBO course on Advanced methods in Bioimage Analysis (EMBL, September 2025). The first slide of his presentation reads "WEBKNOSSOS Visualization, annotation and data sharing of large images".

Norman Rzepka from Scalable Minds (Germany) talks in the EMBO course on Advanced methods in Bioimage Analysis (EMBL, September 2025). The slide of his presentation reads "3D imaging produces increasingly large volumes" and shows some examples of dataset sizes of milestone projects over the past few years.

Norman Rzepka from Scalable Minds (Germany) is presenting in the EMBO course on Advanced methods in Bioimage Analysis (EMBL, September 2025). The current slide of his presentation reads "Render animations" and shows a 3D EM volume and its corresponding neuron segmentation.

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