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Reposted by BoneJ

Jean-Yves Tinevez @jytinevez.bsky.social · 6d

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 · 6d

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

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BoneJ @bonej.org · 6d

🤔

Michael Doube @mdoube.bsky.social · 6d

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 · 6d

🤩

Michael Doube @mdoube.bsky.social · 6d

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 · 7d

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

Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 16d

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 · 20d

#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

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Reposted by BoneJ

Ignacio Arganda-Carreras @iarganda.bsky.social · 9d

📣 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

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Reposted by BoneJ

Siân Culley @superresolusian.bsky.social · 10d

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

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BoneJ @bonej.org · 14d

🦴 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! 📻

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BoneJ @bonej.org · 19d

So bad it's good

Rrrr we love the Ccc

David Shiffman, Ph.D. 🦈 @whysharksmatter.bsky.social · 20d

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 · 23d

📢 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).

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BoneJ @bonej.org · 23d

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).

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Reposted by BoneJ

Guillaume Jacquemet @guijacquemet.bsky.social · 29d

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

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BoneJ @bonej.org · 27d

🔥🔥🔥 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 🤞

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Reposted by BoneJ

The Francis Crick Institute @crick.ac.uk · 27d

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

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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!

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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

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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

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BoneJ @bonej.org · Sep 2

📢 Intel GPUs now supported by BoneJ+ 🤖

Today's new release lets BoneJ+ run on Intel GPUs, which are very common in laptops, in addition to NVIDIA and AMD GPUs. Even antique, 10-year-old ones are working.

Ellipsoid Factor+ is also going 1.5-3× faster.

Just let the ImageJ/Fiji updater run!

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BoneJ @bonej.org · Aug 31

Looking good for a release early this week (CW36)

BoneJ+ will start to work on Intel GPUs and go faster on NVIDIA and AMD too.

BoneJ @bonej.org · Aug 30

😮 BoneJ+ running Ellipsoid Factor on NVIDIA, AMD and Intel GPUs simultaneously!

Look out for this super-helpful update coming soon: BoneJ will start to use GPU acceleration on many (most?) laptops, which have integrated Intel graphics.

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BoneJ @bonej.org · Aug 30

😮 BoneJ+ running Ellipsoid Factor on NVIDIA, AMD and Intel GPUs simultaneously!

Look out for this super-helpful update coming soon: BoneJ will start to use GPU acceleration on many (most?) laptops, which have integrated Intel graphics.

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Reposted by BoneJ

AltYellostoneNatPar @altyellonatpark.org · Aug 30

I should be outa here in a couple days and back at it soon. We study papillomavirus in moose and how they shed the tumors with no scarring and no adverse effects on their reproductive systems.

If you can manage it
Please donate today
gofund.me/babd9034

Donate to Please Support our Research at ALTYNP, organized by Ominous Ann

Having found a research project here in the park, now its up to me to find fundin… Ominous Ann needs your support for Please Support our Research at ALTYNP

gofund.me

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BoneJ @bonej.org · Jul 28

📢Release alert!

BoneJ 7.1.4 is out now, bringing 💥100x faster💥 GPU-accelerated 3D Skeletonization, part of the new BoneJ+ extensions.

You'll need a token to try it out, from bonej.org/shop

Drop us a line [email protected] to get a coupon for a 100% discount on your first token.

bonej.org

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BoneJ @bonej.org · Jul 25

Scratch that:

More like 💥💥100x faster💥💥 !! 🤯

25 seconds vs. 45 minutes

(782x811x549 image, on the laptop+thunderbolt GPU system in the pic above)

Speed improvement is better on bigger images.

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Reposted by BoneJ

Camille Bader @camillebader.bsky.social · Jul 25

🦴 How do proboscidean bones support such massive weight?
Chapter 3 of my PhD is out, a new paper diving into their bone microanatomy!
With Alexandra Houssaye @houssayecnrs.bsky.social and John R. Hutchinson @johnrhutchinson.bsky.social

academic.oup.com/zoolinnean/a...

Professor John R. Hutchinson @johnrhutchinson.bsky.social · Jul 24

Oh! Another paper! From @camillebader.bsky.social Camille Bader's PhD, with Alexandra Houssaye @houssayecnrs.bsky.social. Elephant limb bone microanatomy reflects bone function and posture.
Paper:
academic.oup.com/zoolinnean/a...
Tons of CT scan DICOM files:
figshare.com/articles/dat...

Long-bone microanatomy in elephants: microstructural insights into gigantic beasts

Abstract. One of the greatest challenges of terrestrial locomotion is resisting gravity. The morphological adaptive features of the limb long-bones of exta

academic.oup.com

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BoneJ @bonej.org · Jul 25

Just finished a new GPU-accelerated 3D skeletonization plugin for BoneJ+ that goes 🔥🔥50x faster🔥🔥 than the CPU version, even on an external gaming GPU.

Final testing this afternoon, release next week.

Drop us a line on [email protected] if you'd like a free coupon to try it out!

Development workstation comprising laptop, external GPU connected with Thunderbolt, and a view through trees to the sea.

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