Oh yes-the one and only Robert Haase @haesleinhuepf.bsky.social From #GrandTheftAuto to the impact AI is having on #bioimaging. +the challenges of creating AI courses for bioimage analysis, & his unique perspective as a programmer-turned-biologist. Stream- bit.ly/microscopist... @globias.bsky.social

⭕ This week at @scadsai.bsky.social : We held the 2nd General Assembly in 2025 in Leipzig. The program included talks, workshops, and a poster session. We awarded the "Best PhD Poster Award" to Lea Gihlein, Lea Kabjesz, and Maja Schneider.👏 👉 https://scads.ai/2nd-general-assembly-2025-in-leipzig/

(1/14) I’m happy and proud to introduce: SpinePy – a framework to detect the "spine" of gastruloids and measure biological and physical signals in a local dynamic 3D coordinate system. www.biorxiv.org/content/10.1...

Ensuring reproducibility in GUI-based bio-image analysis tools can be tricky, so I wrote this new blog post on @focalplane.bsky.social. It highlights features in Napari, Fiji, QuPath, Galaxy, CellProfiler and JIPipe that support workflow saving and sharing. Hope it helps! 🤗🔬👩‍💻Feedback 💛ly welcome!

I finally managed to upload the first version of the napari-czitools plugin (still in alpha - expect issues...) - open complete CZI images or subsets - read CZI metadata pypi.org/project/napa... or github.com/sebi06/napar...

Hot off the press!!! Proudly presenting our lab's new review on how do cells communicate to control organ size :) We focus specially on dynamic connections that operate at different timescales to regulate organ growth and morphogenesis. #devbio #SizeandShape www.sciencedirect.com/science/arti...

Ensuring reproducibility in GUI-based bio-image analysis tools can be tricky, so I wrote this new blog post on @focalplane.bsky.social. It highlights features in Napari, Fiji, QuPath, Galaxy, CellProfiler and JIPipe that support workflow saving and sharing. Hope it helps! 🤗🔬👩‍💻Feedback 💛ly welcome!

truly one hour of debugging can save you five minutes of reading documentation

If you seek for an AI coding buddy to review your code and provide umprompted feedback, try out _unprompted_! I hope it helps to identify issues in code early! 🖥️🤖💫 pip install unprompted github.com/haesleinhuep...

Michele Bortolomeazzi, Christian Schmidt and Jan-Philipp Mallm at @nfdi4bioimage.bsky.social have developed a new OMERO-web plugin: OMERO-vitessce. It enables the visualization of datasets hosted in #OMERO with the #Vitessce multimodal data viewer. Find the poster here: 👉 zenodo.org/records/1483...

New ‘How to’ post on FocalPlane 🔬💻 Lea Kabjesz shares a step-by-step guide to get you started annotating 2D and 3D images in Cellpose, including video tutorials. focalplane.biologists.com/2025/06/05/a... #bioimageanalysis #cellpose #imaging #HowTo

Example of why I think current LLMs are enough to change lots of work even if they don’t get better, once we start integrating them with other systems GPT-4 (now obsolete) went from 30% accuracy to 87% accuracy in clinical oncology decisions when given access to tools www.nature.com/articles/s43...

Who does microscopy and has never heard of Bio-Formats? You probably used it anyway

Help! Let’s say I have 200 scientific papers in my digital to-read pile I could stay in denial, or I could ask AI for help. Any workflows/tools to group them in some meaningful way? This alone would help mental load as I at least read abstracts And/or any good summary tools?

I regularly point collaborators at this segmentation quality assurance blog post by @marabuuuu.bsky.social , because some scientists get trapped in a segmentation-improvement-loop without ever measuring how good an algorithm actually is. focalplane.biologists.com/2023/04/13/q...

If you use ML for pixel classification, e.g. using sckit-learn, you can use SHAP analysis for explaining how relevant the feature images are you provided. I just added a Notebook demonstrating how to do this to the #BioImageAnalysisNotebooks 🔬🖥️📈 haesleinhuepf.github.io/BioImageAnal...

Image normalization: trivial enough to automate, impactful enough to quietly sabotage your results. Here’s a Jupyter notebook I wrote on how, why & when normalization matters, feedback 💛ly welcome. 👇 haesleinhuepf.github.io/BioImageAnal...

The YMIA would like to invite everyone interested in microscopy and image analysis to our weekly watch-parties. This Tuesday we cover how to choose the right microscope for your experiment as well as learning how to minimize damage to samples during light microscopy.

#NewGroupPicture #BioImageDataScience #BIDS @scadsai.bsky.social @nfdi4bioimage.bsky.social

In this week’s preprint list, we focus on the latest research in bioimage analysis and data management. Let us know if we are missing any recent preprints that you enjoyed. #bioimageanalysis #datamanagement

Hi everyone! I am searching for a CC-BY 4.0 licensed biological dataset (ideally images but do not have to be) for feature exploration and data visualisation. Ideally, it should be between 100KB and 1GB. Inspiration 💛ly welcome!

Do you want to understand better how LLMs work? Do you want to use LLMs in applications in science or industry? Join us for this two-day training in Leipzig! 🚀

Here we share our opinions on "Practical considerations for data exploration in quantitative cell biology" journals.biologists.com/jcs/article/... Joanna, Hanna and I worked quite a bit on this piece and I hope you find it useful Many thanks to @jcellsci.bsky.social for publishing it

Bioimaging and bioimage analysis friends, some help if you have 2-3 mins; for a paper, we're trying to estimate the number of biologists trained in open source software or tools in the last ~5 years. (1/2) #bioimaging #microscopy #bioimageanalysis

The #gitbob paper has been published in @natcomputsci.bsky.social.🥳 Learn about the path "Towards transparency and knowledge exchange in AI-assisted data analysis code generation" facilitating how humans and AI can work together to solve #dataanalysis tasks. 💽🧑‍🎓🖥️🏗️ rdcu.be/efkna

Are you a student 🧑‍🎓 , group leader 🧑‍🔬 , data manager or imaging facility staff🔬 interested in #imagedata? Join the #EuroBioImaging Image Data Community Days, a FREE, online event taking place from 🗓️ April 7-11 to explore advancements in the field of image data. More 🔽 https://buff.ly/3CHd9uf

The people behind the project globias.bsky.social share a common vision: To bring together data scientists working in microscopy and share their knowledge. scadsai.bsky.social researcher haesleinhuepf.bsky.social and his colleagues about the idea of the project: 👉 www.youtube.com/watch?v=LPJE...

A cartoon I drew a while ago for @gerbi-gmb.de to illustrate the power of research data management in science. Who knows where #RDM and data sharing might lead us to? If even ostriches can fly... 🚀🐥

I recently visited TU Dresden for two guest lectures about Prompt Engineering, RAG, Agents and Multi-Modal #LLMs. thanks to Simon Razniewski @scadsai.bsky.social for having me! My slides are available #openaccess 💻🤖🔓 zenodo.org/records/1469...

As #ScaDS.AI, we're excited to share our research on scalable #datascience and #AI on Bluesky from now on. 🦋 With our two locations, Leipzig University and tudresden.bsky.social, we combine excellent AI, data science and big data expertise. 👉 Follow us: @scadsai.bsky.social

I’m so excited to share my new website with you all! 🎉 Check it out at falk-illustrations.de, explore my artwork, and feel free to reach out if you're interested in commissions or just want to chat! #SciArt #Illustration #NewWebsite #Cartoons #Excited #AndABitProud

Hey #StatsSky, what are you favorite papers to cite when you need to justify something that is obvious (I once had a reviewer ask we justify the use of logistic regression on a binary outcome) or when you need to push-back on silly reviewer requests (e.g., asking for p-values in table 1)?

And to start 2025 strong… Our work #NanoPyx is out in Nature Methods 😍❤️ DOI: doi.org/10.1038/s415... #NanoPyx is a Python framework that uses the #LiquidEngine to efficiently accelerate bioimage analysis for any user! (1/n) ⬇️

In her Essay, Julie Welburn @jwelburn.bsky.social highlights the environmental impact of biomedical research and shares ten easy tips to help reduce your lab’s carbon footprint. journals.biologists.com/jcs/article/...

A little #milestone for the #biabob project: 💯 Github Stars ⭐⭐⭐ 🚀 I'm happy to see the growing community using #biabob as #BioImageAnalysis Coding Assistant in Jupyter. I would love to learn more about what people use it for! Feel free to share screenshots below 😃 github.com/haesleinhuep...

Jeey! @nfdi4bioimage.bsky.social published their #RDM-related postcards FAIRly (made by Henning Falk, licensed CC-BY 4.0) 🔬💾😍 github.com/NFDI4BIOIMAG...

If an #H5N1 pandemic starts tomorrow or in three months, there will be little mystery as to how it happened. The conditions are all there. They have been for a while. So in some ways the more interesting question to me at the moment is: Why aren’t we in a pandemic yet? Story here, 🧵 to come: 🧪#IDSky

My go to for color ideas: thenode.biologists.com/data-visuali... Personally like green, magenta, and orange for microscopy; each channel in grey and then a merged colorized image also recommended.

“We don’t value software, data, and methods in the same way we value papers, even though those resources empower millions of scientists” 💯 www.statnews.com/sponsor/2024...

🧪 Guess the image quiz starts today - Take #ACloserLook 🔎 🎵I see blobs of blue Red circles too I see them move For me and you And I think to myself What could this image be?

thinking of calling this "The Illusion Illusion" (more examples below)

Here are two covers proposals for the current Cell issue, but it didn't make it. I love these renders because they are just data, nothing else! Congrats to @merlinlange.bsky.social & @loicaroyer.bsky.social ! #dataviz #sciart 🐡 🧪 Data imported and rendered in #houdini @sidefx.bsky.social

Our preprint list is now up on FocalPlane. This week we focus on research in #bioimageanalysis. Drop us a message if we’re missing any preprints that you’ve been reading or writing! focalplane.biologists.com/2024/11/29/m...

Voilà! #gitbob and #biabob were updated to support #pixtral, the vision model from the French mistral.ai #LLM provider. It also comes with a free tier 🇫🇷 🇪🇺 🎉 github.com/haesleinhuep... github.com/haesleinhuep...

🤔 Can you turn your vision-language model from a great zero-shot model into a great-at-any-shot generalist? Turns out you can, and here is how: arxiv.org/abs/2411.15099 Really excited to this work on multimodal pretraining for my first bluesky entry! 🧵 A short and hopefully informative thread: