iiinova — where your digital self keeps evolving

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Robert Haase @haesleinhuepf.bsky.social · 26/08/2026

My slides about "How Generative AI impacts [BioImage] Data Science" I presented @mpi-cbg.de yesterday are #openaccess Big thanks for having me! I was a pleasure to be back for the 25th Anniversary of MPI-CBG! doi.org/10.5281/zeno...

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NFDI4BIOIMAGE @nfdi4bioimage.bsky.social · 04/08/2026

Making the Hidden Visible: A fluorescence lifetime imaging dataset shared via RIKEN’s SSBD repository In this month's @nfdi4bioimage.bsky.social calendar, we present a fluorescence-lifetime imaging microscopy (FLIM) dataset by Conni Wetzker, Marcelo Zoccoler, and Gunar Fabig.

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Panos Oikonomou @eigenp.bsky.social · 18/04/2026

1/ 🔬🧑‍💻 Tired of going back and forth between GUIs and code for your 3D image analysis needs? Would you like to keep your focus in one place (notebook), without sacrificing interactivity? Here’s a tool that can help!

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IMAG'IC @imag-ic.bsky.social · 27/05/2026

Join us this Friday, May 29 at 12:00 CET for a #MAIIA webinar! @haesleinhuepf.bsky.social shares his #bioImaging analysis insights zoom : u-paris.zoom.us/j/8906701496... ID: 89067014969 Pass: 285136 #AI #RTmfm @cnrs.fr

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Robert Haase @haesleinhuepf.bsky.social · 12/04/2026

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! ✈️

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Robert Haase @haesleinhuepf.bsky.social · 10/04/2026

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...

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Gaëlle Letort @gaellel.bsky.social · 27/03/2026

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

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eurobioimaging.bsky.social @eurobioimaging.bsky.social · 16/02/2026

📣 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...

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napari @napari.org · 11/03/2026

🔬 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

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CCP-volumeEM @ccp-volumeem.bsky.social · 02/03/2026

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

youtube.com

A brief introduction to the use of containers for reproducible image analysis with Dr Martin Jones

YouTube video by CCP-volumeEM

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Federico Gasparoli @fedegasparoli.bsky.social · 03/02/2026

📣 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! 🧫->🔬->💻->📊

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Jennifer Waters @jencwaters.bsky.social · 06/01/2026

🔬 🖥️ 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

meetings.cshl.edu

Quantitative Imaging: From Acquisition to Analysis

Cold Spring Harbor Laboratory Meetings & Courses -- a private, non-profit institution with research programs in cancer, neuroscience, plant biology, genomics, bioinformatics.

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Brian Northan @truenorth-ia.bsky.social · 19/12/2025

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...

youtube.com

Using Appose with Pixi and Napari for reproducible deep learning segmentation workflows.

YouTube video by Brian Northan

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Florian Jug @florianjug.bsky.social · 28/12/2025

🚨 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/...

janelia.org

Deep Learning for Microscopy Image Analysis

Topics The following will be covered extensively during lectures, exercises, and project work: Image denoising and restoration (fully supervised and self-supervised) Image translation (e.g.,

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Damian Dalle Nogare @damiandn.bsky.social · 08/12/2025

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 💯

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Guillaume Jacquemet @guijacquemet.bsky.social · 27/11/2025

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

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Séamus Holden 🔬🦠🧫 @seamusholden.bsky.social · 24/11/2025

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

forum.image.sc

TrackMate v8 - segmentation editor and Python CLI integration

TrackMate v8: 2D Segmentation Editor & Python CLI Integration Hi everyone, I am excited to announce TrackMate v8, a major update introducing key improvements for both end-users and developers. Mai...

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Jean-Yves Tinevez @jytinevez.bsky.social · 20/11/2025

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:

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David Stansby @dstansby.bsky.social · 04/11/2025

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

ome-zarr-book.readthedocs.io

An Introduction to OME-Zarr for Big Bioimaging Data

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Robert Haase @haesleinhuepf.bsky.social · 23/10/2025

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...

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Jean-Yves Tinevez @jytinevez.bsky.social · 10/09/2025

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). 👇

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FocalPlane @focalplane.bsky.social · 29/08/2025

📢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...

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Omaya Dudin 𓂆 ¦🍉¦🦠¦🔬¦ @dudinlab.bsky.social · 28/08/2025

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

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foundingGIDE @gideproject.bsky.social · 25/08/2025

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

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Sebi @sebi06.bsky.social · 20/08/2025

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...

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NFDI4BIOIMAGE @nfdi4bioimage.bsky.social · 14/08/2025

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...

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India BioImaging @indiabioimaging.bsky.social · 18/07/2025

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...

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Fabrizio Musacchio @fabmusacchio.bsky.social · 11/07/2025

✍️ 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

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Robert Haase @haesleinhuepf.bsky.social · 25/06/2025

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...

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Robert Haase @haesleinhuepf.bsky.social · 26/06/2025

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...

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:

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German BioImaging @gerbi-gmb.de · 23/06/2025

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.

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BIAUnit @biaunit.bsky.social · 17/06/2025

🚀 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

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Robert Haase @haesleinhuepf.bsky.social · 15/06/2025

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...

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Nicolas Chiaruttini @nkiaru.bsky.social · 27/11/2024

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

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FocalPlane @focalplane.bsky.social · 09/06/2025

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

focalplane.biologists.com

Annotating Images in Cellpose - FocalPlane

Annotating Images in Cellpose - How to

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Jean-Yves Tinevez @jytinevez.bsky.social · 11/06/2025

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

journals.plos.org

F-BIAS: Towards a distributed national core facility for bioimage analysis †

Author summary We describe our experience in creating a nationwide core facility offering services in bioimage analysis. This virtual facility federates existing resources scattered across the territo...

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Robert Haase @haesleinhuepf.bsky.social · 01/06/2025

#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...

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Nature Methods @natmethods.nature.com · 14/05/2025

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

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Robert Haase @haesleinhuepf.bsky.social · 20/05/2025

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...

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GloBIAS @globias.bsky.social · 19/05/2025

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...

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Mara Lampert @marabuuuu.bsky.social · 16/05/2025

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...

haesleinhuepf.github.io

Image Normalization — Bio-image Analysis Notebooks

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Robert Haase @haesleinhuepf.bsky.social · 15/05/2025

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...

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Wei-Chen CHU @weichen01.bsky.social · 10/05/2025

📣 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

github.com

GitHub - EABIAS/2025-ImageJ-Micro-Image-Analysis-and-Programming_Taipei

Contribute to EABIAS/2025-ImageJ-Micro-Image-Analysis-and-Programming_Taipei development by creating an account on GitHub.

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Robert Haase @haesleinhuepf.bsky.social · 08/05/2025

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...

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Robert Haase @haesleinhuepf.bsky.social · 06/05/2025

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

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Robert Haase @haesleinhuepf.bsky.social · 02/05/2025

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...

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Nicolas Chiaruttini @nkiaru.bsky.social · 02/05/2025

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).

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