Ignacio Arganda-Carreras
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iarganda.bsky.social
Ignacio Arganda-Carreras
@iarganda.bsky.social
800 followers 400 following 89 posts
Bioimage analysis and computer vision enthusiast. Whenever I can, I do software too.

Ikerbasque | University of the Basque Country (UPV/EHU) | DIPC | Biofisika Institute

ORCID: 0000-0003-0229-5722
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iarganda.bsky.social
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.
September 19, 2025 at 1:02 PM
iarganda.bsky.social
... 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).
September 19, 2025 at 10:47 AM
iarganda.bsky.social
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.
September 19, 2025 at 9:58 AM
iarganda.bsky.social
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.
September 19, 2025 at 9:41 AM
iarganda.bsky.social
Good night!
September 18, 2025 at 6:23 PM
iarganda.bsky.social
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!
September 18, 2025 at 6:23 PM
iarganda.bsky.social
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 😎
September 18, 2025 at 2:48 PM
iarganda.bsky.social
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).
September 18, 2025 at 12:02 PM
iarganda.bsky.social
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.
September 18, 2025 at 9:44 AM
iarganda.bsky.social
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.
September 18, 2025 at 8:32 AM
iarganda.bsky.social
Day 5️⃣ of our @embo.org course on "Advanced methods in bioimage analysis"! 🔬🖥️📊 @embl.org

@tischi.bsky.social is already launching 🚀 Lecture 4: Introduction to working with OME-Zarr (Tutorial) @openmicroscopy.org @zarr.dev
Christian Tischer addresses the online participants of the EMBO Advanced methods in biomage analysis course before starting his tutorial on OME-Zarr. Christian Tischer gets prepared to start his tutorial on OME-Zarr in front a full classroom. Christian Tischer gives the first intructions to the onsite and the online participants of the EMBO Advanced methods in biomage analysis course for his tutorial on OME-Zarr.
September 18, 2025 at 7:23 AM
iarganda.bsky.social
Let's finish the day with the round table discussion 🗣️💬 fantastically led by @ahklemm.bsky.social and Suganya Sivagurunathan from @scilifelab.se & Uppsala University!

So many interesting comments about reproducible science 🧪 and commercial vs open-source software 👩‍💻 in image facility projects 🔬
Panoramic view of the classroom during the round table discussion led by Anna Klemm and Suganya Sivagurunathan from Scilifelab & Uppsala University, Sweden.
September 17, 2025 at 4:07 PM
iarganda.bsky.social
UMAP clustering, points to regions, image features in #AI and #BioimageAnalysis... Where is Wählby/Wally? 😜
September 17, 2025 at 2:37 PM
iarganda.bsky.social
Running 🏃 after lunch we get to the awesome keynote lecture: "Image-based exploration of molecular and morphological components of tissue" by 💫Carolina Wählby💫 from Uppsala University 👇
Carolina Wählby from Uppsala University presenting a slide about the Nature Method of the year (2024): spatial proteomics. Panoramic view of the room where Carolina Wählby from Uppsala University is giving her key lecture to the students of the 2025 EMBO course on advanced methods in bioimage analysis. Carolina Wählby shows a slide that reads "Still struggling with the cell classification problem 20 years later..." during her key lecture to the students of the 2025 EMBO course on advanced methods in bioimage analysis.
September 17, 2025 at 12:38 PM
iarganda.bsky.social
After the coffee break ☕, we continue with the second part of practical session 5, with Nikolai Köhler and Wangjun Hu 🎓 going through the different materials: from storing spatial-omics data 💽 to learning spatial patterns using #MEFISTO 😎
Nikolai Koehler goes over the materials of the first part of the course. Panoramic view of the EMBO course classrom while Nikolai Koehler is talking. Wangjun Hu goes throught the materials of the second part of Practical session 5.
September 17, 2025 at 10:20 AM
iarganda.bsky.social
And here we go again with Day 4️⃣ of the @embo.org course on "Advanced methods in bioimage analysis"! 🔬🖥️📊

We just started "Pratical session 5: Spatial statistics and omics integration" with @brittavelten.bsky.social and her team 💪 from @uniheidelberg.bsky.social ...
Anna Klemm presents Britta Velten (from Heidelberg University) before Practical session 5 (Spatial statistics and omics integration) in the presence of Nikolai Köhler and Wangjun Hu. Britta Velten on stage addressing the course students. Panoramic view of the classroom full of students attending the practical session by Britta Velten, Nikolai Köhler and Wangjun Hu.
September 17, 2025 at 7:24 AM
iarganda.bsky.social
See you all tomorrow! 👋

We hope you enjoyed the ~Spanish~ German tapas and desserts! 😋
September 16, 2025 at 8:33 PM
iarganda.bsky.social
Extremely interesting presentation that ended with an open debate 🗣️ about how/when to decide our results are good enough 👌 and the student's promise that they will follow Beth's checklist ✅ and write down 📝 everything they do on their experiments 🤗
September 16, 2025 at 8:33 PM
iarganda.bsky.social
And we end the lectures of the day with @bethcimini.bsky.social teaching us online about research integrity ⚖️ and "5 pitfalls (especially in #ML) that can lead to disaster" 😱
Students waiting for the online lecture "Reproducible Research - or at least, we hope" by Beth Cimini. Panoramic view of the EMBO course students and instructors attending the online lecture by Beth Cimini about research integrity. The current slide on the two main screens reads "5 pitfalls (especially in ML) that can lead to disaster".
September 16, 2025 at 4:22 PM
iarganda.bsky.social
And we continue with the second part of the session on behavior modeling by learning how to process meshes... Is that the Death Star 🤓? Thanks so much, @kevinyamauchi.bsky.social for joining us online and for a fantastic session! 👏
September 16, 2025 at 3:47 PM
iarganda.bsky.social
Jumping 🕴️ now into "Practical session 4: Behavior Modeling" with @kevinyamauchi.bsky.social online! First things first, students are getting to know how to do #bioimage visualization in Python 🖥️🐍 using @napari.org👇
September 16, 2025 at 12:52 PM
iarganda.bsky.social
... and we keep tracking 👣 with @jytinevez.bsky.social after a delicious coffee break ☕

On-site and on-line, plenty of useful things are been shown and learnt about #TrackMate!
September 16, 2025 at 9:53 AM
iarganda.bsky.social
Day 3️⃣ of our @embo.org course on "Advanced methods in bioimage analysis" at @embl.org with "Practical session 3: Tracking" 🔬🦠🔀.

@jytinevez.bsky.social is already shining at the stage! 🕺🪩.

Important update: #TrackMate v8 is coming! 🤗
Jean-Yves Tinevez addresses the students of the EMBO course to present "Practical session 3: Tracking". Jean-Yves Tinevez shows an slide about "Scientific tools to track cells and organelles", including TrackMate, MaMuT and Mastodon software. Jean-Yves Tinevez shows an slide about TrackMate v8, with bacteria images already segmented. Jean-Yves Tinevez shows an slide entitled "A collection of tracking components at your fingertips", showing a long list of segmentation software including MorphoLibJ, Trainable Weka Segmentation, Ilastik, StarDist, cellpose, and more.
September 16, 2025 at 8:10 AM
iarganda.bsky.social
Good night!
September 16, 2025 at 6:20 AM
iarganda.bsky.social
What better way of celebrating the end of our 2nd day of training classes than with pizza 🍕, refreshements 🍻 and selfies 🤳! 😜
September 16, 2025 at 6:20 AM