New video: more examples showing deep learning segmentation failure modes—and how to detect them with Napari. I show how Napari’s layer system compares images, ground truth, and results, and how Appose enables comparison across incompatible DL packages. www.youtube.com/watch?v=c369...

🚨 Alarm!!! 🚨 AI/ML course for microscopy image analysis!!! 🧐 In 2026 at Janelia (@hhmijanelia.bsky.social), no tuition, housing and meals provided! Isn’t that borderline unbelievable?!? 20 students, ~14 TAs and lecturers 🗓️ June 4-18 2026 ✍️ Jan 15 2026 ✍️ 🔁 pls!! www.janelia.org/you-janelia/...

This would have been a game changer when I was doing microscopy and I suspect will be for lots of people now. Flexible control of commercial microscope systems! Also if you know me I'm often not a fan of cutesy names for software, but "diss track" is 💯

Interested in Zebrafish brain imaging? We released a 3D printed mold that's is super helpful for us. Check it out Customizable FDM-based zebrafish embryo mold for live imaging www.biorxiv.org/content/10.1... Work by Marcela and Jaakko in the lab

New release of the TrackMate single particle tracking plugin for ImageJ by @jytinevez.bsky.social looks amazing! forum.image.sc/t/trackmate-... Loads of new features, most excitingly to me deep learning segmentation algorithms including Omnipose (for cells), and Spotiflow (for spots) #bioimaging

We just released a new major version of TrackMate (v8), the cell and organelle tracking plugin of Fiji. It ships many new features, detailed below, but that are articulated around the following:

Today I'm announcing a new digital textbook 📖🖥️, "An Introduction to OME-Zarr for Big Bioimaging Data". ome-zarr-book.readthedocs.io

I just finished my @unileipzig.bsky.social #LunchLecture. Thanks everyone for the vivid discussion and Nicole Koburger for hosting us! The slides are online #openaccess 🧑‍🏫🔓 zenodo.org/records/1742...

Save the date! The @pasteur.fr Pasteur course on image analysis is announced: It will happen from the 1st of June to the 5th 2026. This year there will be only one track: the Early Career Investigator track (beginners). 👇

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

📢Last few days to apply for this round of our #microscopy training grants with @jcellsci.bsky.social Available to ECRs working on #cellbio to attend a microscopy or bioimage analysis training course. Apply by 5 September www.biologists.com/grants/jcs-f...

A new #UExM probe for #Actin! Fun times thinking/developing/testing with @centriolelab.bsky.social & @lreymond.bsky.social ! Congrats to all ! If interested in #UExM, or #HAK-Actin, feel free to reach out ! Soon available at @spirochrome.com #Expansion #Microscopy #ProtistsOnSky

The #foundingGIDE Community Event 2025 program is now live! 📌 Location: Brisbane, Australia & Online 📅 Deadline: 31st August 📃 Program: docs.google.com/document/d/1... @globalbioimaging.bsky.social @nifaustralia.bsky.social @micro-au.bsky.social @eurobioimaging.bsky.social #imaging #bioimaging

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...

Interested in #bioimaging and #datascience? The "Bio-Image Data Science Lectures 2025 @unileipzig.bsky.social / @scadsai.bsky.social" by @haesleinhuepf.bsky.social offer theory and practice on #Python, #machinelearning, #deeplearning, #LLMs, and research data. 📝 zenodo.org/records/1585...

Launching the #IBIWebinarSeries! Join us for the talk by Prof. Sudipta Maiti, Senior Professor, Dept of Biological Sciences, BITS, Pilani, Hyderabad Campus Title: “Light Microscopy: The Newest Kids on the Block” Time: July 25, 2025 | 3–4 PM IST Register here: uu-se.zoom.us/webinar/regi...

✍️ New in #eLife: #CellSeg3D introduces #WNet3D, a self-supervised 3D #segmentation method for #microscopy data — no labels needed. Claims to outperform #Cellpose/#StarDist on 4 datasets. Includes #opensource plugin (#Napari) + full 3D annotated #cortex dataset. Will test it later. @napari.org#eLife

It was an honor to give a keynote lecture about #VLMs for Bio-Image #DataScience at the @helmholtzimaging.bsky.social #HIconference2025. You find my slides #openaccess 🔬🖥️🚀 doi.org/10.5281/zeno...

I just finished a full-day hands-on tutorial about applications of LLMs as part of the @scadsai.bsky.social Summer School. Big thanks everyone for the lively discussions about prompt engineering, code&data generation, RAG, vision, function calling and #AI agents 🖥🤖🚀 scads.github.io/LLM_Summer_S...

Core facility contributions are essential, and #ImagingScientists deserve to receive #CreditWhereItsDue. That’s why we fully support the #AcknowledgementGuidelines launched by @royalmicrosoc.bsky.social and @globalbioimaging.bsky.social and have proudly displayed them in our digital office.

🚀 Manual mask annotation slowing you down? 💡 SAMJ is a new ImageJ/Fiji plugin using Segment Anything (SAM) for fast, interactive segmentation — no GPU needed, one-click install, real-time results. 🔬 Perfect for large biomedical images. arxiv.org/abs/2506.02783 #AI #Bioimaging #ImageJ #OpenSource

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...

Why #BigDataViewer loves multi-resolution (pyramidal) formats: - Top left: Only high-res data → slow & artifacts when zoomed out. - Top right: Only low-res data → no details when zoomed in. - Bottom: All resolutions → seamless, responsive, beautiful. 🎥 #FijiSc

🎀✨Recording now available ✨🎀 youtu.be/jtDunWK8g1o?...

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

Our paper describing the creation of a nationwide core facility for bioimage analysis if out in @plos Computational Biology! 🎉✌️ journals.plos.org/ploscompbiol... So happy about this paper and how the work turned out. A small thread 👇 #bioimageanalysis #corefacility

#biabob 0.28.0 is out and it comes with support for OpenAI's codex-mini model. I also enabled its vision-support. With this, you can turn screenshots of user-interfaces into functional code - directly within your Jupyter notebook 🤯 github.com/haesleinhuep...

A universal AI-powered pipeline enables precise 3D analysis of cell morphology and topology within organoid structures. www.nature.com/articles/s41...

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...

Next #GloBIAS seminar coming up. Curtis Rueden will present on 'Fiji with Python power'. To get the link please register here: www.globias.org/activities/b...

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...

I gave a hands-on tutorial for Collaborative Working with Git[Hub] at @ubleipzig.bsky.social today. My slides and materials are online #openaccess 🖥️🤝🔓 Thanks for having me! zenodo.org/records/1537...

Don't wonder anymore: github.com/Image-Analys...

📣 The EABIAS "ImageJ Microscopic Image Analysis & Macro Programming" course has wrapped up! 🔓 All resources now freely available under CC-BY license: Slides in English/ Recordings in Mandarin Chinese 🔗 github.com/EABIAS/2025-... #ImageJ #Fiji #BioImaging #OpenScience #EABIAS

My slides about "Research Data Management and Open Science" presented at #AI4Seismology Training School @scadsai.bsky.social , covering the RDM life cycle, FAIR principles, conda environments, software quality metrics and licensing aspects are available #openaccess 💾🖥️🔓 zenodo.org/records/1536...

Together with Max Joas, I gave an introduction to Machine Learning (Unsupervised, supervised, ML, DL) at the #AI4Seismology Training @scadsai.bsky.social . As usual, our slides are available #openaccess 🏔️💻🔓https://zenodo.org/records/15348199

In case you were wondering where the "Tools" menu is gone in @napari.org 0.6.0, please update your environment using "pip install napari-assistant==0.6.0". Then just start "naparia" instead of "napari" from the terminal, while we are working on a better solution. github.com/haesleinhuep...

Hehe, finally had time to revamp a bit Warpy. It's now possible to concatenate a series of transformed sections in a 3D stack for #QuPath. Computed on the fly and with reasonable performance (image and transform field caching).

#GloBIAS has a blog series - new post out today! Two GloBIAS volunteers reflect on the first version of GloBIAS Free Help (previously Call4Help), explain the idea behind this activity and what was learned during the pilot session. Please check out the webpage: www.globias.org/resources/gl...

Finally BiaPy is out in Nature Methods! 🥳🥳🥳 A major milestone in my research! I'm incredibly proud of the progress made. Huge thanks to my PhD supervisors, @iarganda.bsky.social and @arratemunoz.bsky.social , for their invaluable guidance and support throughout this journey. Check out the thread🧵👇

📢 Bio-protocol Webinars present: Next-generation expansion microscopy: 20× magnification in one step 🔗Register now! Join us on: 🗓 Date: May 20, 2025 ⏰ Time: 11:00 AM EST Speaker: Shiwei Wang #Webinar #LifeSciences #Microscopy

Spatially variant deconvolution by Amit Kohli et al: www.nature.com/articles/s41... Can be used advantageously with light sheet fluorescence microscopy.

Please check out BiaPy from Muñoz-Barrutia, Arganda-Carreras, and colleagues for user-friendly deployment of deep learning tools for bioimage analysis. www.nature.com/articles/s41...

Second round of hashtag#GloBIAS Free Help (previously Call4Help) is happening in May. You can register for the sessions on our webpage: www.globias.org/activities/g... Registration deadline is 7. May 2025.

CellPhePy is now available 🎉🎉🎉 in the journal of #microscopy. A python version for #CellPhe. See doi.org/10.1111/jmi.... Thanks @ukri.org and @wellcometrust.bsky.social for funding @globias.bsky.social @globalbioimaging.bsky.social @eurobioimaging.bsky.social @bioimaginguk.bsky.social

When working with label images, we often assume: maximum intensity = number of labels in the image. But if this is not the case, some post-processing algorithms fail. Hence, #stackview 0.15.3 now warns users that these label images are not sequentially labelled 🔬🖥️🤓 github.com/haesleinhuep...

Are you a #BioImageAnalysis pro? Challenge your skills by playing #BIAbubbles! 🎉 Find the right workflows and reproduce the result! 🔬🖥️🕹️ And if you have challenging BIA tasks, new level contributions are welcome! 😀 github.com/haesleinhuep...

New tools! GreenPy and ApplePy are fluorescent biosensors for pyruvate with huge responses (20–40x in vitro) and a range of affinities (10s of μM to mM). These should be game changers for imaging of metabolism! Great work by Shosei Imai @sikmys.bsky.social and team 👏. www.biorxiv.org/content/10.1...

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.