John Bogovic
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bogovicj.bsky.social
John Bogovic
@bogovicj.bsky.social
200 followers 190 following 5 posts
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Reposted by John Bogovic
erickratamero.com
Big news! The Data Management team/Data Science Centre at EMBL (i.e. my team) is hiring for a position based in Heidelberg (but working across all sites!). We are looking for a scientific workflows developer that will focus on multimodal pipelines. embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
Scientific Workflows Developer
The European Molecular Biology Laboratory (EMBL) is Europe’s life sciences laboratory – an intergovernmental organisation with more than 110 independent research groups and service teams covering the ...
embl.wd103.myworkdayjobs.com
January 14, 2026 at 9:37 AM
Reposted by John Bogovic
florianjug.bsky.social
🚨 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/...
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.,
www.janelia.org
December 28, 2025 at 7:06 PM
Reposted by John Bogovic
hannah-haberkern.bsky.social
📢 Join us, the Haberkern lab, @uni-wuerzburg.de for a postdoc studying neural circuit mechanisms of navigation. You’ll spearheading neurophysiology experiments on our brand new 2P!

⏳ Apply by 28th February 2026

Details: www.haberkernlab.de/docs/ENPostd...

#neuroscience #academicjobs #postdoc
On the left, the image shows a schematic of a fly head, ring neurons and EPG neurons together with some calcium imaging frames. On the right is a photo of a fly on a ball in virtual reality and another schematic of a VR system.
December 23, 2025 at 11:27 AM
Reposted by John Bogovic
dddavi.bsky.social
In addition to the Comments linked to below, this news article ("Technology Feature") ties together perspectives from many additional workers in the field, including yours truly: www.nature.com/articles/s41...
December 9, 2025 at 5:13 PM
bogovicj.bsky.social
Do you have 2D-to-3D image registration challenges? Let me know about them here
forum.image.sc/t/toward-bet...
Toward better 2D - 3D registration in BigWarp
BigWarp has so far focused on 2D-2D or 3D-3D registration, and not on 2D-3D registration. After a conversation with @Christian_Tischer , we thought some simple UI changes could make the support for 2...
forum.image.sc
November 29, 2025 at 6:03 PM
Reposted by John Bogovic
joelluethi.bsky.social
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 🧵
Hackathon participants group picture
November 17, 2025 at 1:24 PM
Reposted by John Bogovic
virginieuhlmann.bsky.social
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.
November 13, 2025 at 5:08 PM
Reposted by John Bogovic
joelluethi.bsky.social
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)
Hackathon group picture in the lecture room Hackathon group picture in the restaurant (where not everyone fit on the picture unfortunately) Josh Moore giving a talk at the hackathon Matt McCormick asking a question
November 20, 2024 at 10:31 PM
Reposted by John Bogovic
jo-soltwedel.bsky.social
This is what hacking *actually* looks like. #OME_NGFF_Hackathon
November 12, 2025 at 5:00 PM
Reposted by John Bogovic
dstansby.bsky.social
Today I'm announcing a new digital textbook 📖🖥️, "An Introduction to OME-Zarr for Big Bioimaging Data".

ome-zarr-book.readthedocs.io
An Introduction to OME-Zarr for Big Bioimaging Data
ome-zarr-book.readthedocs.io
November 4, 2025 at 3:33 PM
Reposted by John Bogovic
bethcimini.bsky.social
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...
November 3, 2025 at 10:04 PM
Reposted by John Bogovic
bethcimini.bsky.social
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.
October 31, 2025 at 3:37 PM
Reposted by John Bogovic
dstansby.bsky.social
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. 🟥 ➡️ 🌎
A coordinate transformation graph. Each coordinate system is denoted by a circle, and arrows between systems denote coordinate transformations. Four images named tile_0, tile_1, tile_2, tile_3 have transformations to a "physical" system, and then to a common "world" system.
October 22, 2025 at 9:24 AM
Reposted by John Bogovic
will-j-moore.bsky.social
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!
October 20, 2025 at 1:00 PM
Reposted by John Bogovic
preibischs.bsky.social
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...
October 11, 2025 at 1:30 PM
Reposted by John Bogovic
msschwartz21.bsky.social
#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/
October 7, 2025 at 8:24 PM
Reposted by John Bogovic
hhmijanelia.bsky.social
🪰 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
October 6, 2025 at 2:16 PM
Reposted by John Bogovic
jefferis.bsky.social
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....
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 ...
www.janelia.org
October 5, 2025 at 3:40 PM
Reposted by John Bogovic
carlesbosch.bsky.social
#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
Hard X-ray imaging of biological soft tissues symposium 2025
tinyurl.com
September 23, 2025 at 10:43 AM
Reposted by John Bogovic
agtebo.bsky.social
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...
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 ...
hhmi.wd1.myworkdayjobs.com
September 19, 2025 at 10:05 PM
Reposted by John Bogovic
aafkegros.bsky.social
I gave a talk at Blender Conference yesterday, showing how biological volumes work, and how to visualize them in Blender 😋 youtu.be/WPajSWX730o?... #bcon25
Microscopy Nodes: handling large biological volumes — Blender Conference 2025
YouTube video by Blender
youtu.be
September 19, 2025 at 7:35 AM
Reposted by John Bogovic
herrsaalfeld.bsky.social
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...
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 ...
hhmi.wd1.myworkdayjobs.com
September 18, 2025 at 4:50 PM
Reposted by John Bogovic
volumeem1.bsky.social
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!
Microsoft Forms
forms.office.com
September 10, 2025 at 9:38 PM
Reposted by John Bogovic
danielkrentzel.bsky.social
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...
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...
www.nature.com
September 10, 2025 at 9:37 AM
Reposted by John Bogovic
allierced.bsky.social
github.com/allierc/MPM_pytorch
@HHMIJanelia
pytorch version of github.com/yuanming-hu/...
August 29, 2025 at 11:37 AM