iiinova — where your digital self keeps evolving

Kyle Harrington @kyleharrington.com · 04/08/2026

*debates which torch monitor to use* docs.pytorch.org/docs/2.13/mo... or en.wikipedia.org/wiki/Sago_mo...

en.wikipedia.org

Sago monitor - Wikipedia

020

Reposted by Kyle Harrington

Da-Neng Wang @danengw.bsky.social · 28/07/2026

Congratulations to Ellen Zhong, Princeton University, for receiving the 2026 K.H. Kuo Award for Outstanding Young Scientist in Structural Biology www.bsc.org.cn/KuoSymposium...

1309

Reposted by Kyle Harrington

Aafke Gros @aafkegros.bsky.social · 24/07/2026

Microscopy Nodes 3.1 is out for Blender 5.2! 🎉 This has cool new features for conditional masking, working with even larger data (regional upscaling), and data manipulation! Watch the new youtube tutorials that explain the features: www.youtube.com/playlist?lis...

A FIB-SEM plankton visualization where the top shows only the volumetric data of the chromosomes, and the bottom a normally sliced region of the cell.

A fluorescence microscopy dataset where a region has been reloaded to be much higher resolution

26827

Reposted by Kyle Harrington

SciPy Conference 2026 @scipyconf.bsky.social · 16/07/2026

📣 One of the best parts of #SciPy2026 is seeing the Scientific Python ecosystem evolve in real time. Today's Tools Plenary featured updates from the teams behind Zarr, Xarray, Tiled, Pangeo, scikit-image, Matplotlib, and napari, showcasing new features & future directions 🫶

0164

Reposted by Kyle Harrington

Loïc A. Royer 💻🔬🧪 @loicaroyer.bsky.social · 14/07/2026

📣 Tracking cells through time – including divisions – is a core problem in live-imaging microscopy. We built HOCT, an edge-centric Transformer that hits state-of-the-art on the Cell Tracking Challenge without a pretrained image encoder. Work led by @jookuma.bsky.social arxiv.org/abs/2607.11754 🧪🔬💻

67021

Reposted by Kyle Harrington

Zebrafish Rock! @zebrafishrock.bsky.social · 30/06/2026

Cool opportunity to help the community and get some cash 🤑

153

Reposted by Kyle Harrington

Teun Huijben @teunhuijben.bsky.social · 29/06/2026

🚨Open call to the Cell Tracking crowd out there🚨! Loïc's team at @biohub.org opened our Kaggle Challenge for 3D cell tracking, with $60k of prize money💰. Spread the news, delve into our gigabytes of imaging (zarr3) and cell tracking (geff) data of developing zebrafish embryos, and start tracking 🤩

086

Reposted by Kyle Harrington

Biohub @biohub.org · 29/06/2026

How do you track thousands of cells in complex systems, in 3D & over time? We are launching a Kaggle challenge to push the frontier of AI-powered cell tracking, building on advances like Ultrack & the DaXi lightsheet microscope from the @loicaroyer.bsky.social lab. bit.ly/4bfdzWE

01510

Reposted by Kyle Harrington

Loïc A. Royer 💻🔬🧪 @loicaroyer.bsky.social · 29/06/2026

Fantastic work by the team: Thibaut Goldsborough, Jordão Bragantini, Xiang Zhao, Gordon Leary, Teun Huijben, Ilan da Silva Theodoro, Kyle Harrington, Chi-Li Chiu, Walter Reade, María Cruz.

041

Reposted by Kyle Harrington

Loïc A. Royer 💻🔬🧪 @loicaroyer.bsky.social · 29/06/2026

7/ 💰 $60K prize pool ($18K to 1st) · 🗓️ Final submission Sept 29, 2026 Build the next state of the art in cell tracking and help map life as it unfolds. 🔬🐟 👉 www.kaggle.com/competitions... #CellTracking #Kaggle

kaggle.com

Biohub - Cell Tracking During Development

Detect and track zebrafish cells through 3D space and time

472

Reposted by Kyle Harrington

Loïc A. Royer 💻🔬🧪 @loicaroyer.bsky.social · 29/06/2026

6/ 💻 You don't need to be a biologist. If you're into computer vision, object detection, segmentation, or graph optimization 📊, this is your problem. It's a code competition (notebooks, GPU/CPU ≤12h). Starter data and a sample submission are live now.

122

Reposted by Kyle Harrington

Loïc A. Royer 💻🔬🧪 @loicaroyer.bsky.social · 29/06/2026

5/ 🧠 Why it matters: accurate single-cell lineages power developmental biology, immunology, and disease research 🩺, letting us ask where every cell comes from and where it ends up as a body takes shape. Better tracking = faster, more reproducible science.

121

Reposted by Kyle Harrington

Loïc A. Royer 💻🔬🧪 @loicaroyer.bsky.social · 29/06/2026

4/ 🗺️ This is the problem behind Zebrahub (the Biohub's "Google Earth" of zebrafish development) and Ultrack 📄, our method in Nature Methods 2025 that topped the Cell Tracking Challenge on dense 3D embryos. Now it's your turn to push the state of the art!

151

Reposted by Kyle Harrington

Loïc A. Royer 💻🔬🧪 @loicaroyer.bsky.social · 29/06/2026

3/ ⚠️ Why it's hard: high cell density, imaging noise, and irregular shapes break automated trackers, and small per-frame errors compound into broken lineages. 🪢 Today, scientists fix this by hand, with countless hours of manual tracking. That's the bottleneck.

141

Reposted by Kyle Harrington

Loïc A. Royer 💻🔬🧪 @loicaroyer.bsky.social · 29/06/2026

2/ 🧫 The data: 3D+time light-sheet movies of fluorescently labeled zebrafish embryo cells (~88 GB training data, stored as Zarr). Thousands of similar-looking nuclei moving, deforming, and dividing. Biggest Dataset EVER! Your task: detect every cell, link it across time, and catch every division. ⏱️

141

Reposted by Kyle Harrington

Loïc A. Royer 💻🔬🧪 @loicaroyer.bsky.social · 29/06/2026

1/ 🧬🔬 How does one cell become an entire animal? We can now film it in 3D 🐟, but turning those movies into accurate cell tracks is brutally hard. Enter our new #Kaggle challenge: $60K prize pool, to help crack 3D+time cell tracking at scale! 🧵👇 www.kaggle.com/competitions... @biohub.org

17941

Reposted by Kyle Harrington

Danielle Grotjahn @nanigrotjahn.bsky.social · 16/06/2026

Cryo-ET is often framed as a tool for in situ protein structure. But what if the real revolution is contextualization? I explore how #teamtomo is redefining what "local" means in organelle biology, revealing membrane states rather than just protein structures. tinyurl.com/localmembrane

sciencedirect.com

Think globally, act locally: Redefining organellar membrane environments through cryo-electron tomography

Early enthusiasm for the “cellular revolution” in cryo-electron tomography (cryo-ET) was largely driven by the promise of resolving protein structures…

26323

Reposted by Kyle Harrington

Utz Ermel @uermel.bsky.social · 12/06/2026

You can take a look at a demo tomogram acquired with the xLPP of apo-ferritin on the cryoET data portal here: cryoetdataportal.czscience.com/datasets/10496 Raw data is of course also available for download!

cryoetdataportal.czscience.com

Dataset

0216

Reposted by Kyle Harrington

Biohub @biohub.org · 11/06/2026

In a series of 3 papers and preprints, we’re thrilled to share with you the working laser phase plate. In collaboration with research led by Holger Müller at UC Berkeley, this is a huge innovation in imaging to make small and faint objects inside cells visible. bit.ly/4vK9LVn

Waves of laser light coming from four different directions and meeting in the middle brightly inside the cavity of the laser phase plate

15336

Reposted by Kyle Harrington

Loïc A. Royer 💻🔬🧪 @loicaroyer.bsky.social · 03/06/2026

Want to build some of the most advanced light-sheet microscopes in the world to watch life assemble itself cell by cell? The Royer Lab @ Biohub is hiring an Optical Engineer (Advanced Light Sheet Microscopy). 🧪🔬💻🔧 #Hardware + #Python + Advanced #Optics job-boards.greenhouse.io/biohub/jobs/...

job-boards.greenhouse.io

Optical Engineer, Advanced Light Sheet Microscopy

San Francisco, CA (Hybrid)

02919

Reposted by Kyle Harrington

SciPy Conference 2026 @scipyconf.bsky.social · 03/06/2026

🔬 Tutorial Spotlight: Build custom image analysis tools without starting from scratch. Tim shows you napari's power for microscopy, satellite data, and everything between 🛰️ Extend, visualize, annotate like a pro! #SciPy2026 🔗 scipy2026.scipy.org

0178

Reposted by Kyle Harrington

Nature @nature.com · 27/05/2026

A newly released AI tool has generated an atlas of more than one billion predicted protein structures and billions more protein sequences. go.nature.com/4wS3Pen

go.nature.com

Move over, AlphaFold: open source model predicts shape of 1 billion proteins

The new open-source atlas, generated by an AI tool called ESMFold2, vastly increases the known protein universe.

25517

Reposted by Kyle Harrington

Biohub @biohub.org · 27/05/2026

Proteins are the machinery of life. Billions of their sequences have been cataloged—but the biology behind most is still unknown. Today we're releasing ESMFold2, ESMC and ESM Atlas to help change that. Open source, open to every scientist. biohub.ai/esm/protein

12915

Reposted by Kyle Harrington

napari @napari.org · 22/05/2026

🎉 Announcing the naPLari hackathon in Kraków, Poland 🇵🇱, July 24–29 2026, after EuroSciPy! Hack on napari, join deep dives, meet the team. All experience levels welcome! 📝 Register by July 1: napari.typeform.com/naplari-hack #napari #ScientificPython #OpenSource #EuroSciPy #BioImageAnalysis

napari.typeform.com

naPLari Hackathon

Questionnaire for the napari hackathon in Krakow, Poland, July 24-29th, 2026.

176

Reposted by Kyle Harrington

arXiv cs.CV Computer Vision and Pattern Recognition @cscv-bot.bsky.social · 06/05/2026

Grigory Solomatov, Derya Akkaynak: Conditions for well-posed color recovery in scattering media arxiv.org/abs/2605.03837 arxiv.org/pdf/2605.03837 arxiv.org/html/2605.03837

011

Reposted by Kyle Harrington

Biohub @biohub.org · 29/04/2026

Today we're announcing the Virtual Biology Initiative—a major new commitment to build the data foundation biology needs to power the next generation of AI models. Next-gen imaging. Molecular engineering tools. Open data infrastructure for the entire scientific community. Read more: bit.ly/3ONTkHO

bit.ly

Biohub launches the Virtual Biology Initiative

A $500M commitment to galvanize a global, open-data effort to build predictive models of the human cell.

095

Kyle Harrington @kyleharrington.com · 20/04/2026

Also noting that copick is a great example of impactful work that is enabled here at @biohub.org!

020

Reposted by Kyle Harrington

Utz Ermel @uermel.bsky.social · 20/04/2026

Excited to share our paper about copick, a dataset API and toolkit for collaborative annotation and analysis of #cryoET data! Whether you're picking particles or curating segmentations, copick reduces friction and brings #OME-Zarr to cryoET without breaking pipelines. 🧵👇 doi.org/10.1002/pro.70578

19230

Reposted by Kyle Harrington

Utz Ermel @uermel.bsky.social · 20/04/2026

Big thanks to all co-authors, collaborators, and early testers! @danielji.bsky.social @zhuowenzhao.bsky.social @kyleharrington.com @rahelwoldeyes.bsky.social

051

Reposted by Kyle Harrington

Utz Ermel @uermel.bsky.social · 20/04/2026

Done with annotation? Use copick-torch for PyTorch-compatible data loading to train your model! Docs, tutorials, and code at 👇 🔗 copick.github.io/copick/ 🐧 github.com/copick

copick.github.io

copick - copick

121

Reposted by Kyle Harrington

Utz Ermel @uermel.bsky.social · 20/04/2026

copick includes an MCP-server and batch curation tools: describe your curation pipeline in plain language, let an AI agent compose a curation pipeline for you. No coding required.

A figure showing an example prompt and the generated script.

131

Reposted by Kyle Harrington

Utz Ermel @uermel.bsky.social · 20/04/2026

copick works across storage backends: local filesystems, HPC, S3/cloud, or directly from the cryoET Data Portal. Plugins for @chimerax.ucsf.edu and @napari.org handle all the details, so multiple users can annotate the same data simultaneously. No overwriting, no headaches, easy import/export.

A diagram showing the full copick workflow, from obtaining data from the cryoET portal to deposition of new or curated annotations.

151

Kyle Harrington @kyleharrington.com · 20/04/2026

Woohoo, copick is out! Access to massive amounts of CryoET data, MCP for agentic, plus a @napari.org interface! We even used it when hosting the CZII CryoET Kaggle competition: www.kaggle.com/competitions... when we needed to support a large collaborative annotation event with humans + ML models.

kaggle.com

CZII - CryoET Object Identification

Find small biological structures in large 3D volumes

0184

Reposted by Kyle Harrington

bioRxivpreprint @biorxivpreprint.bsky.social · 16/04/2026

A generative AI framework for disease-specific lung microtissue bioengineering www.biorxiv.org/content/10.64898/20…

011

Reposted by Kyle Harrington

bioRxiv Bioengineering @biorxiv-bioeng.bsky.social · 16/04/2026

A generative AI framework for disease-specific lung microtissue bioengineering www.biorxiv.org/content/10.64898/20…

011

Reposted by Kyle Harrington

AI x Bio Discovery @aixbiobot.bsky.social · 16/04/2026

A generative AI framework for disease-specific lung microtissue bioengineering [new] ...leverages 3D tissue imaging and diffusion models to design and bioprint anatomically detailed lung models for preclinical applications.

011

Reposted by Kyle Harrington

Levayer Lab @levayerr.bsky.social · 27/03/2026

Happy to share the heroic effort of @gaellel.bsky.social to reduce our segmentation pain through EpiCure (Epithelial Curation), a napari plugin easing the curation of epithelial segmentation developed with several groups of @devstempasteur.bsky.social. www.biorxiv.org/content/10.6... See more 👇

biorxiv.org

14218

Reposted by Kyle Harrington

napari @napari.org · 24/03/2026

napari 0.7.0 is available now! 🚀🎉 It's a BIG release so read the full release notes, with highlights: napari.org/stable/relea... We want to thank everyone who has worked incredibly hard on this release including our 11 new brilliant contributors 🤩 and the community for their support and feedback!

napari.org

napari 0.7.0

Mon, Mar 23, 2026 We’re happy to announce the release of napari 0.7.0! napari is a fast, interactive, multi-dimensional image viewer for Python. It’s designed for browsing, annotating, and analyzing…

14420

Reposted by Kyle Harrington

Leah Lavery @helloleahlavery.bsky.social · 23/03/2026

Congratulations to Dr. Julia Mahamid on receiving the 2026 Gottfried Wilhelm Leibniz Prize! 🎉 Her pioneering work in cryo-ET is reshaping our understanding of how molecular architecture drives cellular processes and disease. #teamtomo #LeibnizPrize #StructuralBiology #LifeSciences #Innovation

dfg.de

Julia Mahamid, Ph.D. – Gottfried Wilhelm Leibniz Prizewinner 2026

06111

Kyle Harrington @kyleharrington.com · 18/03/2026

This looks awesome! Some gifs would be super cool 😉

020

Reposted by Kyle Harrington

Image Cooperative @image.coop · 16/03/2026

Hello, world! We are starting a worker cooperative to build, maintain, teach, and support open source scientific imaging software. image.coop/blog/posts/2...

88444

Reposted by Kyle Harrington

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

12720

Reposted by Kyle Harrington

Utz Ermel @uermel.bsky.social · 27/01/2026

New on the CryoET Data Portal: ~27,000 tomograms of affinity-captured lysosomes from HEK293T cells across 4 physiological states. Includes raw data, AreTomo3 reconstructions & Membrain-Seg annotations. Openly available for reuse! cryoetdataportal.czscience.com/depositions/...

Four representative slices of cryo-tomograms showing annotated organelles.

17321

Reposted by Kyle Harrington

Andrew G. York @andrewgyork.bsky.social · 23/01/2026

Thanks, Rita! I was pretty darn happy that the journalists at Nature (and Science) were kind enough to write up the story of Maria's discoveries. I appreciate y'all, it really helps our mission. www.nature.com/articles/d41...

nature.com

‘Remote controlled’ proteins illuminate living cells

The discovery that some fluorescent proteins are sensitive to magnets could lead to the development of switchable drugs and biosensors.

2124