Happy New Year YMIA! Another full year has come to an end: we hosted microscopy watchparties, joined key imaging conferences & organized a panel on Open Data in Bioimage Analysis (available soon on YouTube) In 2026, expect invited talks on practical image analysis & more opportunities to connect🍀🥂🔬🎉

Two new articles from our lab!! Davis et al identified epithelial transcription factor ELF3 as a key mediator of host-microbiota interaction in zebrafish tinyurl.com/pkavnxdp Morash et al revealed enteroendocrine cell subtypes in zebrafish & catalogued their peptide hormones tinyurl.com/bdzbm2xm

Teaching Academic life to cats, lesson 301: Funding Opportunities 💸🐈

🔬 Latest GerBI Team Meeting @MPIMF & EMBL Heidelberg We asked: 🌟 Why does GerBI exist? 🚀 What defines us? We’re currently turning these insights into statements & will bring them to life together 🌟 Welcome to our new team members & thanks to Elisa D'Este & Stefan Terjung for their hospitality!

Volumetric near-infrared light-sheet imaging of a calcium indicator (WHaloCaMP) in a zebrafish larval brain. Credit to @helenfarrants.bsky.social, William "Bill" Lemon, & Philipp Keller at @hhmijanelia.bsky.social. #ZebrafishZunday 🧪

✨A gut feeling you’ll love this one 🐛 The anterior midgut of a Drosophila melanogaster 🪰larva puts on a confocal glow show! 🟢 Adult midgut progenitors 🔴 Actin 🔵 Nuclei 📸Image by Sapna Krishnakumar #FluorescenceFriday #Microscopy #DevBio

Starting the day with a motivational quote in the restroom at work. 🌞

Enteric Neurons Join the Dialogue on Pain! A recent study reveals that cholinergic circuits within the colon communicate through dorsal root ganglion (DRG) pathways, particularly following inflammation. 👉 www.cell.com/neuron/fullt...

I won't talk about NMeth @natmethods.nature.com forever (probably), but I do want to brag a bit about the November focus issue on cell segmentation and tracking, which is many ways is my last hurrah (and final editorial) for the journal. I am so proud of these papers!! www.nature.com/nmeth/volume...

Bis jetzt war ja alles grau. Aus diesen riesigen Datensätzen können wir 3D Modelle der Zellen erstellen. Eins davon seht ihr hier (Erstellt von meiner Kollegin Deborah Schmidt). Wie wir von den Rohdaten zu diesen 3D Abbildungen kommen, werde ich euch diese Woche zeigen.

Fluorescent micrograph of the enteric nervous system of a Pachon/surface hybrid cavefish. Credit to @pavaniperera.bsky.social. #ZebrafishZunday 🧪

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

London moves into the spotlight for #NeuroGASTRO2025 🌈🌈 Meet me at poster AI-03 to talk about how we're shedding light on #ENS research 🐟🔬 💻

Just out of the oven onlinelibrary.wiley.com/doi/10.1111/... I’m so excited! Stay tuned for more posts about it and give it a read when you can🥰

After we lost our beloved cat Pixel earlier this summer, we decided to increase our catabilities: Please welcome Oskar (left) and Kiwi (right) #kittens 🐈🐈‍⬛️

Burnout is clinically understood as a combo of 6 factors—work overload, lack of control, insufficient rewards, breakdown in community, absence of fairness, & value conflicts—and only a fraction of it is under your control. Burnout is a systemic problem, so be kind to yourself and hard on the system.

Got questions about the #HelmholtzImaging Project Call? Ask everything you need to know at our next info session on Thursday, July 17, 11:00 to 12:40 PM CEST. Learn how #HIFIS can support your project, too. Details & registration 👉 events.hifis.net/event/2663/ @helmholtz.de #HIProject #imaging

Forschende unter Leitung des #UFZ haben #Nanoplastik in allen Tiefenzonen zwischen gemäßigter und subtropischer Zone im Nordatlantik gefunden. Massenmäßig ist die Menge vergleichbar mit dem, was bisher an #Mikroplastik gefunden wurde, schreiben sie im Fachmagazin @Nature. www.ufz.de/index.php?de...

Looking for new #microscopy collaborations, organising speakers for a conference, assembling a committee? Visit and join the @focalplane.bsky.social network to broaden your contacts and find those who may not come to mind. focalplane.biologists.com/network #Microscope #Imaging #CellBiology

Generate beautiful PDF of your manuscripts easily using Markdown. #RxivMaker is here. We hope it will supercharge your #preprints Mojo.

🔬 YMIA is at the Helmholtz Imaging Conference 2025! Elena from the core team presents a poster about the YMIA community — who we are, what we do, and how we connect early-career researchers in imaging and analysis. She’s here to exchange ideas and meet you. Come say hi! #HIConference2025 #BSIC2025

Great vibes, exciting science! 🐟 Today, the #zebrafish community in @helmholtz.de met for the 1st time at #HIconference2025. We kicked things off with energy, ideas & tools for better zebrafish #imaging. Thanks to all who joined & our co-hosts @ufz.de & BER at @kit.edu! #HelmholtzImaging #FAIRdata

I gave in! After students asking for it, I now made a simple figure design checklist. To help all scientists w/o graphic skills create clear, accessible, and truthful charts! -> Out in @nature Cell Biology: rdcu.be/erwl4 #DataVisualization #PhD #SciComm Thx for review @bethcimini.bsky.social + 2

ICYMI #zebrafish folks: Fresh from ‪@lascholz.bsky.social‬ and Conrad Lee, we offer 4 models pre-trained with diverse fps and resolutions. Leandro’s done all of the clicking. Benefit from his suffering and plug straight into automated annotation of your videos!‬ www.biorxiv.org/content/10.1...

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...

Helmholtz turns 30 – and shares 30 inspiring stories from across the @helmholtz.de. Today’s spotlight: the Helmholtz Information & Data Science platforms – including #HelmholtzImaging, @helmholtzai.bsky.social, HIDA, HIFIS & HMC. Read more 👇 #Helmholtz #Helmholtz30 #DataScience #imaging

Scott Glaberman, Chris Frey and I lay out why EPA's Office of Research and Development should be protected, not destroyed. Please share widely. Dismantling EPA’s research office jeopardizes environmental safety, public health, and US competitiveness | PNAS www.pnas.org/doi/10.1073/...

A reason I go to conferences is to promote image data managment. I tend to repeat myself a little, so here's my elevator speech in memes.

Can you go from protein sequence to a generated image of protein localization? New work from the Uhler lab says yes, and it is generalizable to unseen proteins and more than one cell type. I'm excited for work moving us toward virtual cell models.

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...

Do you work with large image datasets? Discover our optimized workflows for efficient metadata annotation and #FAIR data management. 🔬💻

Please take a moment to appreciate the beautiful imaging art that was submitted this year 😍 (also, can you spot my image?)

I am slowly loosing my mind over this #Fiji / #ImageJ plugin... I want to use Noise2Noise, but it keeps giving me this error code 403... I checked the internet but couldn't find anything that helped me in this situation. I am sure swarm intelligence here knows the issue 😀 #cellbio #microscopy

Interested in Developmental biology? Imaging? Marine invertebrate body plans? Then this three year postdoc in my group @sotonbiosciences.bsky.social is for you! Join our team to decypher how signalling molecules shape skeletal phenotype in juvenile sea urchins. jobs.soton.ac.uk/Vacancy.aspx...

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.

🚀🔬🦠 Releasing 🤖Cellpose-SAM🤖, a cellular segmentation algorithm with superhuman generalization 🦸‍♀️. Try it now on 🤗 huggingface.co/spaces/mouse... paper: www.biorxiv.org/content/10.1... w/ @computingnature.bsky.social 1/n

Need help with image analysis? Now's your chance, with the upcoming Free Help event from Globias! Find out more and register with the link below👇

GloBIAS #BioimageAnalysis #Conference 2025 – we have opened the registration for our 2025 in-person event. Please check the webpage www.globias.org/activities/b... for more information and the link to the registration form.

If image processing was about bubbles... 🫧

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!

Your yearly reminder to acknowledge the core facilities you use and their staff scientists in your papers. These scientists are a crucial part of the scientific ecosystem and to continue to exist they need tangible credit for their work. Plus their associated expertise adds credibility to your work.

🌍 On April 8-9, the #ENDOMIX consortium got together in #Rotterdam to reflect on our progress and engage in fruitful discussions. With valuable feedback from our Stakeholder Board, the consortium is driven to move forward in uncovering the hidden health risks of #EDCs! #HorizonEU #EUfunded @ufz.de

Preparations for #TiM2025 are in full swing! The name badges are ready, and we are excited to welcome all our participants next week! ✨

If, hypothetically, a person were trying to set up a career panel series for bioimage analysis, what kinds of roles (or specific people) would you want to hear more about? Hypothetical nominations of all stripes welcome :) #bioimageanalysis

Fantastic NEWS! The successful BioVoxxel workshops will step-by-step become available as online self-learning courses. Scientific Illustration is the first one released and 4 more will follow. Check out the course page: www.biovoxxel.de/individual-w... Enjoy the teaser video youtu.be/qvMHTZAOCrA

Happy to share that our latest work is out now! BMP signaling pathway member expression is enriched in enteric neural progenitors and required for zebrafish enteric nervous system development @thedrjam.bsky.social @rodrigomorec.bsky.social anatomypubs.onlinelibrary.wiley.com/doi/10.1002/...

Dr. Jo Nyffeler @ufz.de was awarded £300K to develop innovative approaches to reduce animal testing in avian #toxicity studies. In cooperation with ESQlabs GmbH they will analyze existing data to integrate #NAMs into regulatory environmental risk assessments: nc3rs.org.uk/crackit/news...

For World Birth Defects Day, I highlight the birth defect my lab studies using zebrafish as an animal model, Hirschsprung Disease #HSCR. www.niddk.nih.gov/health-infor...

#biabob, the AI-based code generator for Jupyter Notebooks, can now be configured to generate code for other scientific domains🔭, coding-styles 🎭 and languages🗣️. Handle with care, as you can also use this to do stupid things. 😉 Feedback welcome🚀 pip install bia-bob==0.26.0 github.com/haesleinhuep...

Very excited to host @danielgorelick.bsky.social at @ufz.de @ufz-cite.bsky.social for a deep dive into EDC mode of action delineation in #zebrafish.