Lightnews — Scholar-powered news

BoneJ @bonej.org · 15h

🔥🔥🔥

Reposted by BoneJ

Michael Doube @mdoube.bsky.social · 2d

Gotta admit, I'm pretty excited about this one. GPU-accelerated Local Thickness, for Tb.Th and Tb.Sp. This is the plugin in the @bonej.org logo, made MUCH faster by re-engineering for GPU parallelism.

Drop me a PM to get a token to try it out for free.

BoneJ @bonej.org · 2d

1

BoneJ @bonej.org · 2d

2

BoneJ @bonej.org · 2d

The CPU implementation has a problem of thickness spheres overhanging the input mask by a pixel, introducing some inaccuracy. This GPU implementation has a more accurate Euclidean distance transform giving the sphere-fitting higher fidelity to the input geometry and less orthogonal grid bias.

BoneJ @bonej.org · 2d

Small structures are also problematic as ever. But what's the thickness of a 1-pixel-wide line? The answer is much more meaningful for features represented by at least several pixels' thickness (what is several you may ask, well, try it and see...).

BoneJ @bonej.org · 2d

Smaller simpler images now complete in a few seconds or less, depending on image size and feature size.

Unconstrained 'outside' is still challenging, but is now handled by treating it as spheres seeded from the image borders with a radius equal to the distance to the nearest feature in the image.

BoneJ @bonej.org · 2d

Large structures could make Tb.Sp in particular seem to run forever, or least longer than you would reasonably wait. 😴

Try it now. Big structures are still challenging, but should be done in like 1 hour instead of a week.

3

BoneJ @bonej.org · 2d

📢 Release announcement!

Local Thickness+ brings GPU-accelerated Tb.Th and Tb.Sp, for much faster measurements.

Now out in BoneJ.

Just let the updater run, and grab a token from bonej.org/shop to make it go. Drop us a PM to get a coupon for a free token.

2 1 1

Reposted by BoneJ

Jean-Yves Tinevez @jytinevez.bsky.social · 12d

Do you want to work with Michalis and us on a fun and ambitious LSFM, tracking and gamification project?
Apply!!

Michalis Averof @michalis-averof.bsky.social · 12d

Cool collaborations on light sheet microscopy @huiskenlab.bsky.social, cellular barcoding @mgrillo.bsky.social, AI-based cell tracking @jytinevez.bsky.social, and citizen science through video game for cell tracking @rebelpixel.fr

see www.averof-lab.org/pages/tracman

3/3

3 8

BoneJ @bonej.org · 12d

🤔

Michael Doube @mdoube.bsky.social · 12d

Long, slender trabeculae pass across the marrow space. Trabeculae help resist weightbearing loads. But these ones don't appear to be in a good configuration to do that, unlike the spongy trabeculae nearby.

Maybe they're holding adipose tissue in place, preventing it from wobbling during locomotion?

BoneJ @bonej.org · 12d

🤩

Michael Doube @mdoube.bsky.social · 13d

The leftovers from last week's bœuf bourguignon. This is a 'marrow bone' after boiling out the adipose tissue for gravy and washing in lots of warm tap water, household detergents and a little chlorine bleach. Cortex & (glorious) trabeculae, growth plate 'scar', marrow cavity visible.

BoneJ @bonej.org · 13d

Signed up! Come along and get an intro on BoneJ's features.

Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 22d

Halfway to I2K is BACK, friends of all kinds! Last year, 650 people attended 30+ TOTALLY FREE image analysis workshops of all kinds, across many timezones.

If you make image analysis software and want to teach it, workshop submissions are open now! We'd love to have your tool highlighted.

BioImaging North America @bioimagingna.bsky.social · 26d

#HappyFluorescenceFriday!

#microscopycommunity- want to learn open source image analysis or share your knowledge to help others? We’ve got a FREE virtual workshop Nov 17-19! Now accepting workshop session applications!

Learn more & sign up: buff.ly/esGIotD

1 1

Reposted by BoneJ

Ignacio Arganda-Carreras @iarganda.bsky.social · 15d

📣 We’re hiring, please RT! Fully funded 4-year PhD position in our CVPD group at @informatikaehu.bsky.social!

Research at the intersection of AI, deep learning & bioimage analysis. 🧠🔬

📅 Applications open Oct 6 (deadline: ~Oct 27)
📍 San Sebastian, Spain.
👉 cvpd.github.io/post/2025-09...

📢 Open 4-year PhD Position in Deep Learning for Bioimage Analysis! | CVPD Research group

The Computer Vision and Pattern Discovery (CVPD) group at the University of the Basque Country (UPV/EHU) is offering a fully funded 4-year PhD position within the recently awarded project TOSBI: Towar...

cvpd.github.io

2 26 26

Reposted by BoneJ

Siân Culley @superresolusian.bsky.social · 17d

BioImage analysis friends - King's are recruiting for a full-time, permanent facility position! Come and work with fun microscopes and fun people (and me!) - please share! www.kcl.ac.uk/jobs/126345-...

Bioimage Analysis Specialist | King's College London

www.kcl.ac.uk

80 61

BoneJ @bonej.org · 21d

🦴 Up next for BoneJ+: GPU-accelerated Local Thickness.

The classic version is widely used for measuring trabecular thickness and separation (Tb.Th, Tb.Sp), but suffers from g.o.i.n.g v.e.r.y s.l.ow. on images with large or unbound features.

Looking at a release in October: stay tuned! 📻

1

BoneJ @bonej.org · 26d

So bad it's good

Rrrr we love the Ccc

David Shiffman, Ph.D. 🦈 @whysharksmatter.bsky.social · 26d

What’s a pirate’s favorite computer programming language?

You’d think it’s R, but no, their first love will always be the C.

Happy talk like a pirate day!

a man with a beard is wearing a pirate costume and laughing .

ALT: a man with a beard is wearing a pirate costume and laughing .

media.tenor.com

BoneJ @bonej.org · 29d

📢 GPU-accelerated Anisotropy now in BoneJ+

The fabric tensor expresses the scale and orientation of textures like trabecular bone and other porous materials.

Runs on GPUs from Intel, NVIDIA and AMD, 10-100× faster than the classic version 🔥🔥🔥

Get a token from bonej.org/shop to try it out!

Anisotropy+ measures the fabric tensor (yellow lines), a description of the underlying orientation in a porous solid like trabecular bone (white).

1

BoneJ @bonej.org · Sep 16

Getting closer... Anisotropy+ working well in testing, even on antique Intel laptop GPUs, going at least 10× faster than the CPU version. Release coming soon!

3D output of BoneJ's Anisotropy+ plugin showing a piece of trabecular bone from an emu (white) alongside the mean intercept length point cloud or "rose plot" (blue), the fabric tensor (yellow lines) and the grid of points used to sample the image (yellow dots).

1

Reposted by BoneJ

Guillaume Jacquemet @guijacquemet.bsky.social · Sep 10

Come and work with us 5-year position available for a University Researcher in Bioimaging 1.11.2025-31.12.2030

abo.rekrytointi.com/paikat/index...

University Researcher in Bioimaging / Universitetsforskare med inriktning bioimaging, 1.11.2025-31.12.2030

abo.rekrytointi.com

38 35

BoneJ @bonej.org · Sep 12

🔥🔥🔥 Upcoming plugin for BoneJ+, Anisotropy+ running on Intel, NVIDIA and AMD GPUs at the same time!

This one uses fields of line probes to determine the fabric tensor and calculate the degree of anisotropy, a measure of underlying texture orientation and scale.

Looking good for release next week 🤞

2 2

Reposted by BoneJ

The Francis Crick Institute @crick.ac.uk · Sep 12

Want to enhance your image analysis skills with napari?

We’re running a two-day training event on how to use napari to effectively analyse your bioimaging data.

🕒 Applications close on 15 September.

Learn more and apply 👇

www.crick.ac.uk/whats-on/cbi...

CBIAS napari workshop 2025

www.crick.ac.uk

20 23

BoneJ @bonej.org · Sep 6

Next up for BoneJ+:

GPU accelerated mean intercept length for measuring anisotropy via the fabric tensor, used to find directionality in trabecular bone 🦴 and other porous materials (soil, rock, food,..) 🫧🪨🍦

Kernel drafted, host code integration under way... 🧑‍💻

Stay tuned!

1 1

Reposted by BoneJ

Horizons Magazine @horizons-en.bsky.social · Sep 5

Images are often crucial to research. We’ve spoken with three people who make images
accessible to scientists and scholars. 👇
#Microscopy @EPFL_en #ImageArchive #DataViz

www.horizons-mag.ch

2 2

BoneJ @bonej.org · Sep 3

Today's Intel laptop GPUs (like the A770M or Arc Pro A30M) are 10-20× faster than the 10-year-old HD 515 in our testing machine.

www.videocardbenchmark.net/compare/3341...

Intel HD 515 vs Radeon RX 7600M XT vs RTX A4000 vs Intel Arc A770M vs Intel Arc Pro A30M [videocardbenchmark.net] by PassMark Software

www.videocardbenchmark.net

BoneJ @bonej.org · Sep 3

Note though that GPU performance is very different among models. There's a ~10× difference between the fastest and slowest on the daily test system (Dell 7370 laptop with external AMD and NVIDIA cards), which chimes with crowdsourced benchmark data:

www.videocardbenchmark.net/compare/3341...

Intel HD 515 vs Radeon RX 7600M XT vs RTX A4000 [videocardbenchmark.net] by PassMark Software

www.videocardbenchmark.net

1 1