John Bogovic

#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

Male CNS Connectome 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 ...

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....

Hard X-ray imaging of biological soft tissues symposium 2025

#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

AI Engineer - Metabolic Sensor Design Primary Work Address: 19700 Helix Drive, Ashburn, VA, 20147 Current HHMI Employees, click here to apply via your Workday account. Intro: AI@HHMI: HHMI is investing $500 million over the next 10 years ...

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...

YouTube video by Blender Microscopy Nodes: handling large biological volumes — Blender Conference 2025

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

AI Engineer - Evolutionary Protein Language Models Primary Work Address: 19700 Helix Drive, Ashburn, VA, 20147 Current HHMI Employees, click here to apply via your Workday account. Intro: AI@HHMI: HHMI is investing $500 million over the next 10 years ...

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!

CLEM-Reg: an automated point cloud-based registration algorithm for volume correlative light and electron microscopy - Nature Methods CLEM-Reg automates the three-dimensional alignment of volume correlative light and electron microscopy datasets by leveraging probabilistic point cloud registration techniques for fast and accurate re...

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/...

Visual of segmented human induced pluripotent stem cells with the key workshop dates: Symposium on November 10-11, Hackathon on November 12-14th in Zurich Switzerland

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

Image quality metrics fail to accurately represent biological information in fluorescence microscopy Image processing methods offer the potential to improve the quality of fluorescence microscopy data, allowing for image acquisition at lower, less phototoxic illumination doses. The training and evalu...

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...

New BigDataViewer and ImgLib2 Demos Available in Fiji Hi everyone, Just a quick note to let you know there are some new demos available that use BigDataViewer and ImgLib2 to explore a range of datasets, both real and simulated. You’ll find them under Pl...

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
🗓️ 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...

Fundamentals: What Is Zarr? A Cloud-Native Format for Tensor Data - Earthmover What Zarr is, and how it enables fast, scalable access to multidimensional array data in the cloud.

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

OME 2025 - YouTube OME 2025 from April 28 - May 1 at Marine Biological Laboratory in Woods Hole, MA

(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

YouTube video by Ask Erin, Dear Beth AskErinDearBeth Episode 3 - QC on High Content Imaging Datasets using CellProfiler and FIJI

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

Apply | aicjanelia Apply to use the advanced microscopes housed at the AIC.

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!