Do you have 2D-to-3D image registration challenges? Let me know about them here forum.image.sc/t/toward-bet...

We had an amazing OME-NGFF hackathon last week, Wednesday to Friday, following the inspiring OME-NGFF symposium. What a fantastic week! It’s hard to describe how motivating it is to be surrounded by so many talented, curious & friendly people who care deeply about open, FAIR bioimaging data. 1/14 🧵

We wrapped up the symposium part of our 2025 International OME-NGFF workshop on Tuesday. What a phenomenal two days! I'm humbled by the incredible positive energy, talent, and enthusiasm that filled this event.

This week, we're hosting the #OME_NGFF_Hackathon 2024 at the BioVisionCenter at the University of Zurich. We're bringing together 40 motivated researchers and specialist for #OMEZarr workflows, #OMEZarr Python tools & #OMEZarr Java tools. (1/3)

This is what hacking *actually* looks like. #OME_NGFF_Hackathon

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

Do you want to learn more about 25+ bioimage analysis tools, 100% for free? Sign up to attend Halfway to I2K today! tinyurl.com/Halfway-to-I... Wishing you'd submitted a tool or workshop but missed the deadline? GREAT NEWS, we just extended one week! Submit by Friday - airtable.com/app2zpB8d82r...

Registration for Halfway to I2K is now OPEN! And workshop submission is still too (for a bit)! Join 20+ presenters and counting, and hundreds of attendees in learning about image analysis, whether you're a complete beginner or a total pro.

Over at `ome-zarr-models` we're working on implementing support for the new coordinate systems too - here's an example of a transformation graph from multiple tiled images that can be transformed into a common "world" coordinate system. 🟥 ➡️ 🌎

The #OME-Zarr RFC-5 proposal allows you to transform multiple images into the same coordinateSystem. Trying this out with napari at github.com/will-moore/n.... Cool that you can offset T-dimension as well as XYZ!

The connectome of the entire male Drosophila central nervous system is out!! Acquired using FIB-SEM @ 8x8x8nm, we aligned 7.5 mio 2D images aligned into one seamless 3D volume, which was used to segment & proofread neurons and synapses. @hhmijanelia.bsky.social www.biorxiv.org/content/10.1...

#geff v1 is released! 🎉 GEFF is a zarr-based Graph Exchange File Format with special support for tracking applications in Python and Java. Thank you to all the amazing developers who contributed at the Janelia 2025 Trackathon! liveimagetrackingtools.org/geff/

🪰 A team of researchers has unveiled the complete connectome of a male fruit fly central nervous system—a seamless map of all the neurons in the brain and nerve cord of a single male fruit fly and the millions of connections between them. 🔗 https://hhmi.news/4o3EJnk

Exciting news for #drosophila #connectomics and #neuroscience enthusiasts: the Drosophila male central nervous system connectome is now live for exploration. Find out more at the landing page hosted by our Janelia FlyEM collaborators www.janelia.org/project-team....

#Nanoimaging symposium @crick.ac.uk! At #CrickXrays25 we'll tackle: 💫synchrotron upgrades 📈current limits in throughput, volume, resolution 🧪sample preparation for X-ray PC imaging 🧠♥️applications in neuroscience and tissue life science 🗓️13th October 2025 🇬🇧🌐 London & online tinyurl.com/crickxrays25

We are recruiting for a project extending our current work using machine learning for fluorescent biosensors at Janelia! We have both experimental and computational positions posted: hhmi.wd1.myworkdayjobs.com/en-US/Extern... hhmi.wd1.myworkdayjobs.com/en-US/Extern...

I gave a talk at Blender Conference yesterday, showing how biological volumes work, and how to visualize them in Blender 😋 youtu.be/WPajSWX730o?... #bcon25

We are looking for an #AIEngineer to help build protein language models that capture evolutionary constraints with @matsen.bsky.social and @jbloomlab.bsky.social at #AI@HHMI @hhmijanelia.bsky.social hhmi.wd1.myworkdayjobs.com/en-US/Extern...

LAST CALL! Please take the anonymous, 10-minute survey so we can learn more about the computational needs of the volumeEM community: forms.office.com/e/eMAJGCKUnc The survey will close on Friday 19th September, so make sure your voice is heard!

Super happy to see CLEM-Reg out in @natmethods.nature.com! A short thread on the algorithm behind it and how to try it out for yourself🧵(1/9) www.nature.com/articles/s41...

github.com/allierc/MPM_pytorch @HHMIJanelia pytorch version of github.com/yuanming-hu/...

We're happy to announce the 2025 International OME-NGFF workshop 🎉 📅 Dates: - Symposium: Nov 10–11, 2025 - Hackathon: Nov 12–14, 2025 📍 Location: Zurich, Switzerland Full details & registration: www.biovisioncenter.uzh.ch/en/events/Up...  #bioimaging #openscience #OMENGFF #OMEZarr (1/x 🧵)

Once is an exception, twice is a trend, thrice is a tradition! Save the date for our now-traditional annual OME-NGFF extravaganza in Zurich! Whether you’ve just heard about OME-NGFF and are curious to learn more or if you are working with it every day, there is something for everyone this year!

It was a good experience to step back and briefly take stock of the amazing progress in connectomics since I started working on this stuff (20 years ago!) thanks as well to @natrevneuro.nature.com for the constructive editorial interactions.

How is the nervous system organized to coordinate behavior? To approach this massive question, a team led by @asbates.bsky.social, @jasper-tms.bsky.social, @mindyisminsu.bsky.social, & Helen Yang present the BANC: a Brain and Nerve Cord connectome. Preprint: doi.org/10.1101/2025... 🧪#Neuroskyence

Hello! Very excited to share our latest preprint, which is great news for us but terrible news for any diehard fans of PSNR and SSIM as image quality metrics in microscopy... (1/5) www.biorxiv.org/content/10.1...

Hey, it's out! doi.org/10.1016/j.ce... Aligning Big Brains and Atlases, ABBA in short, is published in Cell Reports @cp-cellreports.bsky.social . @biancasilvalab.bsky.social's lab added an analysis pipeline on top of it (BraiAn) and did all the relevant biological work. What is it ? Short thread:

Super excited to announce a follow-up to the Janelia 'mechanistic basis of foraging' conference - this time held in Birmingham, UK! Join us from the 3rd - 5th November to discuss all things foraging: uobevents.eventsair.com/the-mechanis...

I've put some BigDataViewer demos in #Fiji 's PTBIOP update site. Check them out ! forum.image.sc/t/new-bigdat...

Are you looking to advance your bioimage analysis skills? Then don't miss the deadline for #EMBOBioImage 🔬✨ 📩 Apply by 4 June ➡️ https://s.embl.org/bia25-01-bl#EMBOBioImage🗓️ 14 – 19 September 📍 EMBL Heidelberg and Virtual

In the context of our @reviewcommons.org revision process, I'm happy to announce Microscopy Nodes v2.2.0! This packs lots of new fun features, including new color management 🌈, clearer transparency handling 🫥, custom default settings 🔧 and more! Preprint at doi.org/10.1101/2025...

Our latest fundamentals blog post provides an overview of @zarr.dev and its open-source ecosystem. Read more: earthmover.io/blog/what-is...

(almost) every talk from OME 2025 is now on YouTube! If you care about microscopy data and about open-source, you should definitely check them out. www.youtube.com/playlist?lis...

Episode 5 - sure, most cells have one nucleus, but what happens when they DON'T? @erinweisbart.bsky.social and I try to get to the bottom of what on earth you can do when your cells and nuclei just don't match up on the latest episode of "Ask Erin/Dear Beth"

Any scikit-image fans in Vienna? The skimage team would like to meet in Vienna for a code sprint Aug 14-16 ahead of EuroSciPy. We'd super appreciate it if someone's workplace can host us! All we need is electricity, natural light, and (most important) walking distance to coffee. ☕️😂🙏

You can now apply until the 4th of June !! #EMBOBioImage www.embl.org/about/info/c...

FREE Help with Bioimage Analysis!

#HappyFluorescenceFriday #microscopycommunity. @bioimagingna.bsky.social was at OME205 with @openmicroscopy.org this past week with the makers of BioFormats. OME-TIFF, OME-Zarr and OMERO sharing their work and listening to your challenges.

The STIM paper is out! We build on established computer vision techniques to automatically create 3D volumes of spatial transcriptomics datasets with human-level accuracy, and useful, interactive visualizations. www.sciencedirect.com/science/arti... @hhmijanelia.bsky.social @mdc-bimsb.bsky.social

Now out: Episode 3 of Ask Erin/Dear Beth in which @bethcimini.bsky.social and I overview the method we use for QC on high content imaging datasets. It's great for ~*~vibes~*~ and to QC segmentation along with catching debris, confluency, or focus issues. youtu.be/5pAcdd_Nn00

The latest AIC Call for Proposals is now open! Deadline is June 16, 2025. Come use @hhmijanelia.bsky.social imaging technology and expertise for FREE. Visit www.aicjanelia.org/apply for details. Before applying, contact us to schedule a technical consultation!

I know there's a 𝒍𝒐𝒕 going on right now, but I couldn’t be prouder to share this long-incubated labor of love: the complete connectome of the male 𝐷𝑟𝑜𝑠𝑜𝑝ℎ𝑖𝑙𝑎 optic lobe 🧠🪰 🔗 www.nature.com/articles/s41...

🪰A connectome of the fruit fly visual system & classification of its 53K neurons unlock new possibilities for probing vision in fruit flies hhmi.news/3XyqYCy 🔗Read more about these #openscience tools from our FlyEM Project Team & collaborators, first published as a 2024 #preprint: hhmi.news/4iIsavL

Registration deadline is coming up FAST - you have until April 7th!

🪰A new study details a valuable collection of tools for fruit fly researchers made possible by Janelia’s FlyLight Project Team & collaborators➡️ hhmi.news/3QJYuls 🔗Read our story about this "greatest hits" collection from when it was released in a preprint in 2024➡️ hhmi.news/41EXaGU #OpenScience

🚀 We’re very excited to share our latest preprint on OME-Zarr! 🚀 Our report on the 2024 OME-NGFF Workflows Hackathon is a deep dive into the status of OME-Zarr and the great work that happened last November at the BioVisionCenter in Zurich. 🔗 Read the preprint: osf.io/preprints/bi... 🧵 (1/15)

Happy #FluorescenceFriday! #microscopycommunity. Join the Open Microscopy Community meetings #OME2025 at MBL, MA, April 28-May 1. Register today buff.ly/3CYC0tS to join the conversation on image data sharing & formats ...BioFormats, OME-Zarr... @bioimagingna.bsky.social @openmicroscopy.org

We read "Large Concept Models" in our reading group. It models language at the sentence resolution - "concepts". We had lots of thoughts about it! You can read them in our new Janelia CVML blog post: janelia-cvml.github.io/blog/posts/L... #ML #AI #Janelia @adjavon.bsky.social @bogovicj.bsky.social

📢 Submissions are now open for the CellMap Segmentation Challenge. Build the best method for segmenting cellular organelles in vEM using our 289 annotated volumes, 40 organelle classes, and 22 diverse cell and tissue types. 🔗 hhmi.news/410evJQ

Coming soon... 🤩 EMBO Practical Course: Advanced methods in #Bioimage Analysis 🧪📉🔬🦠🖥️