Vision [Language] Embeddings are a powerful tool to dive into relationships between images. If you enjoy traveling through them in 3D as much as I do, try out Vision Embedding Space Traveling (VEST)!
github.com/ScaDS/vest
Bon voyage! ✈️
My lecture recording about "How Generative Artificial Intelligence Impacts BioImage Data Science" I gave at @danishbioimaging.bsky.social / Uni Copenhagen is now online! Big thanks to @claraprats.bsky.social, Sonia Diaz Garcia and colleagues for recording and sharing!
www.youtube.com/watch?v=Nw40...
I'm happy to present our new tool, EpiCure, a napari plugin to ease correction of segmentation and tracking of epithelia movies, developed in @devstempasteur.bsky.social
📣 Registration for the #EuroBioImaging Image Data Community Days is open! Join us for online event centered on bioimaging & preclinical imaging data.
🗓️ April 13-17, online
All are welcome!
Register here ⤵️
www.eurobioimaging.eu/events/image...
🔬 Registration is open for our pilot Introduction to napari Workshop!
napari is a powerful open-source image viewer for scientific data analysis in Python. This hands-on workshop will get you exploring multi-dimensional datasets fast.
#napari #Python #ImageAnalysis #DataScience #OpenSource
Our first 'Show & Tell Series' webinar, presented last week, is now available on YouTube.
Watch here: www.youtube.com/watch?v=E-pi...
We hope it’s useful to the community - please share with anyone who may be interested #VolumeEM #Bioimaging
📣 We are accepting applications for the 2026 Boston Bioimage Analysis Course (BoBiAC): bobiac.github.io! Join us this July at Harvard Medical School for a 6-day intensive hands-on course to learn bioimage analysis with Python!
Apply by May 18th! No prior Python experience required!
🧫->🔬->💻->📊
🔬 🖥️ Applications are open for the CSHL course Quantitative Imaging: From Acquisition to Analysis (April 6–21, 2026)!
An intensive, hands-on course covering advanced fluorescence microscopy and quantitative image analysis using open-source tools.
🗓️ Apply online by Jan 30, 2026
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:
Great! Thank you so much!
Thank you for this wonderful resource! Would you be open to providing a license declaration so others can benefit from your excellent work? We'd love to use it for educational purposes!
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
Microscopy Training Grants Supporting microscopy training for early-career researchers in cell biology Apply for a grant of up to £1,000 Cartoon of a person looking down a microscope, which is next to a computer Journal of Cell Science logo and FocalPlane logo
📢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
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...
ScaDS.AI Summer School LLM Training This is a collection of Jupyter Notebooks about basic and advanced LLM usage, focusing on what’s practicslly possible with Large Language Models. We demonstrate most utilities using the ScaDS.AI Large Language Models (LLM) Servicer (TU Dresden VPN required). Most exercises should also work with other providers such as GWDG KISSKI and Helmholtz Blablador. The tutorial aims at Python programmers who want to dive into LLMs for generating text, code and data using open source/weights models. After this course they will be able to integrate LLMs into their software applications. Contributions and feedback are very welcome! In case you see room for improvement, please create a github issue and/or consider contributing. Topics The notebook collection aims covering these topics: Large Language Models (LLMs) Text/Code/Data generation Prompt Engineering Retrieval-augmented-generation Vision Function calling Agents Covered Python libraries and software In these notebooks we use libraries from the GenAI field: bia-bob llama-index ollama openai Slide decks Also training slides can be downloaded from zenodo: https://doi.org/10.5281/zenodo.15743126 Videos The materials provided here were also discussed in a couple of recorded Online Lectures Large Language Models for Bio-image Analysis (ScaDS.AI Living Lab lecture 2024) Large Language Models – an introduction for life scientists (GloBIAS Seminar 2024) Bio-image Analysis Code Generation (I2K Conference 2024) Generative Artificial Intelligence for Bio-image Analysis Related resources The notebooks presented here were partially taken from other places or inspired by code in these resources:
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.
