iiinova — where your digital self keeps evolving

Ignacio Arganda-Carreras @iarganda.eurosky.social · 19/09/2025

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.eurosky.social · 19/09/2025

... 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.eurosky.social · 19/09/2025

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.eurosky.social · 19/09/2025

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.eurosky.social · 18/09/2025

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.eurosky.social · 18/09/2025

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.eurosky.social · 18/09/2025

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.eurosky.social · 18/09/2025

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.eurosky.social · 18/09/2025

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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Ignacio Arganda-Carreras @iarganda.eurosky.social · 18/09/2025

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.

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Ignacio Arganda-Carreras @iarganda.eurosky.social · 17/09/2025

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.

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Ignacio Arganda-Carreras @iarganda.eurosky.social · 17/09/2025

UMAP clustering, points to regions, image features in #AI and #BioimageAnalysis... Where is Wählby/Wally? 😜

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Ignacio Arganda-Carreras @iarganda.eurosky.social · 17/09/2025

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.

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Ignacio Arganda-Carreras @iarganda.eurosky.social · 17/09/2025

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.

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Ignacio Arganda-Carreras @iarganda.eurosky.social · 17/09/2025

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.

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Ignacio Arganda-Carreras @iarganda.eurosky.social · 16/09/2025

See you all tomorrow! 👋 We hope you enjoyed the ~Spanish~ German tapas and desserts! 😋

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Ignacio Arganda-Carreras @iarganda.eurosky.social · 16/09/2025

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 🤗

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Ignacio Arganda-Carreras @iarganda.eurosky.social · 16/09/2025

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".

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Ignacio Arganda-Carreras @iarganda.eurosky.social · 16/09/2025

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! 👏

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Ignacio Arganda-Carreras @iarganda.eurosky.social · 16/09/2025

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👇

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Ignacio Arganda-Carreras @iarganda.eurosky.social · 16/09/2025

... 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!

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Ignacio Arganda-Carreras @iarganda.eurosky.social · 16/09/2025

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.

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Ignacio Arganda-Carreras @iarganda.eurosky.social · 16/09/2025

What better way of celebrating the end of our 2nd day of training classes than with pizza 🍕, refreshements 🍻 and selfies 🤳! 😜

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Ignacio Arganda-Carreras @iarganda.eurosky.social · 16/09/2025

We finished the (intense) @haesleinhuepf.bsky.social practical session with more advanced strategies using bia-Bob, such as transforming our code into a #Netxflow workflow! 🤓

Students making questions to Robert Haase.

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Ignacio Arganda-Carreras @iarganda.eurosky.social · 15/09/2025

We keep up with the cool stuff! 😎 Now, thanks to @haesleinhuepf.bsky.social and his bia-Bob, we started to play with #LLMs and #BioimageAnalysis scripts in Python on "Practical session 2: Using AI and natural language processing to help image analysis" 🤖💬🖥️🔬📊... More after the coffee break! ☕😋

Robert Haase teaching students about bia-Bob, a Jupyter-based assistant for interacting with data using large language models which generate Python code for Bio-Image Analysis (BIA): https://github.com/haesleinhuepf/bia-bob

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Ignacio Arganda-Carreras @iarganda.eurosky.social · 15/09/2025

And, after lunch 🥪, we keep going with the super interesting "Lecture 1: Women in science" by @perrinegil.bsky.social 💪💜, learning about her personal path in #BioimageAnalysis and how to promote gender equality in the field 🙆‍♀️📊🖥️🔬

Full class of students attending the Women in Science talk by Perrine Paul-Gilloteaux.

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Ignacio Arganda-Carreras @iarganda.eurosky.social · 15/09/2025

Day 2️⃣ of our @embo.org course on "Advanced methods in bioimage analysis" 🔬🖥️🧫 at @embl.org with "Practical session 1: Image Analysis workflow and data management" 💽📊 with the awesome @virginieuhlmann.bsky.social 🤩 Let's the fun start! 💫

Full room of students for the first practical session of day #2 at the Advanced methods in bioimage analysis EMBO course at EMBL.

Christian Tischer gives instructions to students in the classroom of the second day of the Advanced methods in bioimage analysis EMBO course at EMBL.

List of students and training positions for the Advanced methods in bioimage analysis EMBO course.

Virginie Uhlmann addresses the students on the second day of the Advanced methods in bioimage analysis EMBO course at EMBL.

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Ignacio Arganda-Carreras @iarganda.eurosky.social · 27/11/2024

I will 😅 My desktop is not far from that, but the window view is, let's say, less ideal, although it could be (I'm in building 7 in the picture) 🤔

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Ignacio Arganda-Carreras @iarganda.eurosky.social · 27/11/2024

This is an image of what DALL-E 🖌️🎨 thinks my workspace and research environment are based on my interactions with ChatGPT... Not bad at all 😳 Funny how it still struggles with text, except with "Deep learning" for some reason 😅

AI-generated image with the following prompt: "A dynamic scene of a researcher’s workspace combining elements of academia and innovation. The room includes a desk with a dual monitor setup displaying intricate bioimage analysis, deep learning algorithms, and 3D microscopy data. Nearby, a stack of scientific journals and open notebooks sit alongside a coffee cup. The backdrop has a whiteboard covered with colorful diagrams, flowcharts, and project notes related to leukemia diagnosis and Upper Palaeolithic hand stencils. Shelves hold books on AI, biology, and physics, with a potted plant and a few personal touches, such as a framed photo or inspirational quote. A window offers a view of San Sebastian’s green hills and coastline, emphasizing a balance of focus and creativity."

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Ignacio Arganda-Carreras @iarganda.eurosky.social · 23/11/2024

So I tried the word soup of scholargoggler.com and I have to say I wasn't aware of my obsession with image segmentation 🙈😂

Image representing the main keywords from the titles of the publications of Ignacio Arganda-Carreras. The most prominent ones are "segmentation", "deep", "learning", "images", "analysis", "nerual" and "registration".

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Ignacio Arganda-Carreras @iarganda.eurosky.social · 20/11/2024

and 4️⃣, on Friday at 10:45am (Sala Toledo), I will be presenting the history and current state of @biapyx.bsky.social with my talk "BiaPy: Bioimage Analysis workflows for all audiences", see you all there! 😊 #SPAOM2024

Title slide of the presentation by Ignacio Arganda-Carreras at SPAOM 2024, entitled "BiaPy: Bioimage Analysis workflows for all audiences".

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Ignacio Arganda-Carreras @iarganda.eurosky.social · 20/11/2024

3️⃣ Tomorrow after lunch (16.15h – 17.15h, Workshop rooms), @arratemunoz.bsky.social, Lenka Backová, @aaitorg.bsky.social and I will give a community workshop on @biapyx.bsky.social, our deep learning library and application for #BioImageAnalysis #SPAOM2024

Outline of the community workshop on BiaPy at the SPAOM 2024. It reads:
16:15-17:15:
Introduction to BiaPy
What is a workflow
Deep learning recap
What is (and what’s not) BiaPy
BiaPy workflows
Use case: 2D instance segmentation
Top-down vs Bottom-up approaches
Demo with BiaPy notebook
Helpers:
Lenka Backová
Aitor González-Marfil
Arrate Muñoz-Barrutia

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Ignacio Arganda-Carreras @iarganda.eurosky.social · 20/11/2024

2️⃣ Tomorrow as well at 2pm (Zocodover, poster session), my PhD student Lenka Backová will present her work on "Bioimage analysis and biophysical modeling of multicellar systems" with an application on wound healing. #SPAOM2024

Teaser of the poster presented by Lenka Backová at SPAOM 2024 on Bioimage Analysis and Biophysical modeling of multicellular systems.

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Ignacio Arganda-Carreras @iarganda.eurosky.social · 20/11/2024

🧪🔬 Are you at #SPAOM2024 ? Here you have a list of the contributions from my lab (all in Day 2 and 3)👇 1️⃣ Tomorrow at 10:15am (Sala Toledo) my PhD student @aaitorg.bsky.social will present his work "Zero-Shot Object Detection with Foundational Models: A Similarity-Based Approach"

First slide of Aitor González-Marfil's presentation at SPAOM 2024, showing the title "DinoSim: Zero-Shot Object Detection and Segmentation with Foundation Models"

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Ignacio Arganda-Carreras @iarganda.eurosky.social · 20/11/2024

and 4⃣, on Friday at 10:45am (Sala Toledo), I will be presenting the history and current state of @BiaPyX with my talk "BiaPy: Bioimage Analysis workflows for all audiences", see you all there! 😊

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Ignacio Arganda-Carreras @iarganda.eurosky.social · 20/11/2024

2⃣ Tomorrow as well at 2pm (Zocodover, poster session), my PhD student @Lenka_Backova will present her work on "Bioimage analysis and biophysical modeling of multicellar systems" with an application on wound healing. #SPAOM2024

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Ignacio Arganda-Carreras @iarganda.eurosky.social · 20/11/2024

🧪🔬 Are you at #SPAOM2024 ? Here you have a list of the contributions from my lab (all in Day 2 and 3)👇 1⃣ Tomorrow at 10:15am (Sala Toledo) my PhD student @AAitorG will present his work "Zero-Shot Object Detection with Foundational Models: A Similarity-Based Approach"

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Ignacio Arganda-Carreras @iarganda.eurosky.social · 20/11/2024

2️⃣ When processing both images with the model, it seems that the output is the same. However, when the absolute difference is computed, we can notice that it is only the same in the halo, where the convolutions are influenced by the padding and not the content of the image.

Two 256x256 pixel-sized images side by side showing the result of the prediction of the model over the null image and unitary point image. Images are displayed with the viridis colormap from matplotlib, so values near zero are purple and values near one are yellow. At first sight, both images are equal, with values near 1.0 (yellow).

Image displaying the absolute differences between the two previous images. Values are displayed with the viridis colormap from matplotlib, so values near zero are purple and values near one are yellow. We can observe pixels in a 162x162 centered box contain non-zero intensity values while the rest of the image has zero values. That's the size of the halo, i.e., the field of view of the CNN.

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Ignacio Arganda-Carreras @iarganda.eurosky.social · 20/11/2024

1️⃣ Two images that are almost the same are analyzed. The first one is a null image (all-zero values) and the second one is a null image with a centered unitary pixel.

Two 256x256 pixel-sized images, side by side. The image on the left is a "null image" where all its pixels contain an intensity value of zero. The image on the right is a null image with a single pixel with intensity one at its center (128, 128). Images are displayed with the viridis colormap from matplotlib, so values near zero are purple and values near one are yellow.

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Ignacio Arganda-Carreras @iarganda.eurosky.social · 20/11/2024

Thanks for sharing! 🤗 Following a smilar line of thought, we calculate the "halo" or field of view of our CNNs, so we know how far from the edges ⬅️➡️ we need to be, in order to avoid the effect of that padding. In case anybody is interested, here it is how we do it 👇

Image showing the "halo" or "field of view" of a convolutional neural network. The figure represents a 256x256 pixel image where pixels in a 162x162 centered box contain non-zero intensity values while the rest of the image has zero values. The image is displayed with the viridis colormap from matplotlib, so values near zero are purple and values near one are yellow.

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Ignacio Arganda-Carreras @iarganda.eurosky.social · 26/10/2023

Oh! Our work #CartoCell was selected for the cover of the latest @CellRepMethods issue! Such a nice first time for me and @lmescu 🥳 Beautiful artwork by @CarmenMGordill1 and @jasanroman 🤗 Find the full issue here: www.cell.com/issue/S2667-2375(22)X0…

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Ignacio Arganda-Carreras @iarganda.eurosky.social · 15/09/2023

Back at home after an amazing week in the #EMBOBioImage course @EMBLEvents I feel blessed to be part of the fantastic #BioimageAnalysis community 🤗

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Ignacio Arganda-Carreras @iarganda.eurosky.social · 12/09/2023

Four parallel awesome software lounge sessions at our Workshop #EMBOBioimage @EMBLEvents 🔬📊👨‍💻👩‍💻 thanks to @perrinepgil 🤩

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Ignacio Arganda-Carreras @iarganda.eurosky.social · 11/05/2023

Always a pleasure to listen to @gomez_mariscal talking about @deepImageJ, @AI4LifeTeam, and more at the @NEUBIAS_ open symposium in Porto 🤩

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Ignacio Arganda-Carreras @iarganda.eurosky.social · 10/05/2023

Full room @NEUBIAS_ Defragmentation Training School 2 to learn about #BIAflows with @sebastien_tosi 🤓📊🔬

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Ignacio Arganda-Carreras @iarganda.eurosky.social · 04/11/2022

Three open positions (2 postdoc, 1 engineer) at my former lab in @ijpb_fr (Versailles, France) with the fantastic Philippe Andrey. Apply! #BioimageAnalysis ijpb.versailles.inrae.fr/en/researc…

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Ignacio Arganda-Carreras @iarganda.eurosky.social · 28/09/2021

Not to forget, this is also part of the fantastic Bioimage Model Zoo initiative, with @ilastik_team @ImJoyTeam #ZeroCostDL4Mic @FijiSc and more friends! bioimage.io

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