Join me for a tutorial on @bonej.org 17 November 13h00 CET

ImageJ/Fiji users will be pleased to know that opening a DICOM stack with File > Import > Image Sequence results in correctly calibrated z pixel spacing. DICOM slice position (0020,0032) and not slice thickness (0018,0050) fields are used to determine the size of the image stack.

It also speaks to the good scientific hygiene of taking some basic measurements from the physical specimens using tape, ruler or caliper, and including standard objects in the image to use as calibration sanity checks prior to later image analysis. DON'T ASSUME THE INSTRUMENT IS PROPERLY CALIBRATED

OMG this is a good catch. We wrestled with this a long time ago when setting up Slice Geometry. The correct way to set slice spacing (pixel spacing in z) from a DICOM is to use the slice position info (0020,1041 or 0020,0032) and divide by (stack size - 1). It can be out by not much or quite a bit.

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Want to automate workflows in #FIJI? Don't know where to start? We (@lankylaste.bsky.social, Alicja Skórkowska and Sara Salgueiro Torres) have added a step-by-step tutorial to the wiki to get you started. Thanks @ctrue.bsky.social for adding! imagej.github.io/tutorials/ba...

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.

📢 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.

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

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

📣 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...

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-...

🦴 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! 📻

So bad it's good Rrrr we love the Ccc

📢 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!

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!

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...

🔥🔥🔥 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 🤞

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...

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!

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

📢 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!

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+ 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.

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

📢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.

🦴 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...

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!

[Crocodile Dundee voice] THAT's a 3D model of trabecular bone. Spotted in @horizons-en.bsky.social 145 Concrete moulded around an ice form, meant for low-frequency urban noise filtering. Could be almost any other open-cell foam TBF, but looks like bone to me! www.revue-horizons.ch/2025/06/05/d...

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Working with @globalbioimaging.bsky.social, we're very proud to launch our new #AcknowledgementGuidelines poster, helping #ImagingScientists get the credit they deserve for their research contributions! #CreditWhereItsDue @bioimaginguk.bsky.social Read more: rms.org.uk/resource/rms...

Register now for #ICVM2025 online & see our keynote talks: Faysal Bibi, Museum für Naturkunde Berlin, Germany Anne Claire Fabre, Univ. Bern, Switzerland Tiana Kohlsdorf, Univ. São Paulo, Brazil Karen Sears, Univ. California LA, USA Neil Shubin, Univ. Chicago, USA www.isvm-icvm.org/icvm-2025

📢Navigating Strategies for Core Facilities 2025: A Town Hall Webinar (16 June, 5-8pm BST) Don't miss this *free*, interactive webinar to help shape the future of core facilities! 🔬 Join the discussion - all are welcome😀 #imaging #microscopy rms.org.uk/rms-event-ca... @rmsearlycareer.bsky.social

Busy month coming up! Annual Meetings and workshops at: SBMS: 13 June, Interlaken docs.google.com/forms/d/e/1F... SwissBIAS: 18-19 June, Bern www.eventbrite.ch/e/swissbias-... BRS: 25-27 June, Edinburgh boneresearchsociety.org/meeting/brs2... See you there!

2009!

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I like spotting when buildings look like what they do inside. Biology buildings with 'spiral' staircases, because DNA is a double helix, that kind of thing. This is the roof of the AO Center in Davos. The AO Foundation is into bone screws, and so... (see it?)

☀️ Le #mimosa, un brin de soleil en hiver, mais... Cette espèce originaire d'Australie est envahissante en France. ⚠️ En raison de sa multiplication rapide, elle entre en compétition avec la flore indigène et modifie le milieu. Les espèces invasives en 5 questions 👉 www.mnhn.fr/fr/les-espec... #EEE

Amazing news on thr #Fiji front. The new launcher holds beautiful promises for better bioimage analysis tools, and not only for Fiji!! See this summary thread by Curtis forum.image.sc/t/fiji-2024-...

The people behind the project globias.bsky.social share a common vision: To bring together data scientists working in microscopy and share their knowledge. scadsai.bsky.social researcher haesleinhuepf.bsky.social and his colleagues about the idea of the project: 👉 www.youtube.com/watch?v=LPJE...

I am recruiting an #ERC funded PostDoc to work on the evolution of vertebral counts in cichlids. This is an experimental project & will be looking for candidates with experience generating reporter lines, live-imaging and experimental embryology. Application deadline: 25th Feb. tinyurl.com/33jbu8fa

Main reason I’m in Zimbabwe is to work out if this ‘Massospondylus’ material (a selection of the tons they have) is really Massospondylus or something else. Sounds dull but has implications for dating & correlating rocks in Zim with those in South Africa & dino diversity 🦖🇿🇼🦕

Answering the call of @haesleinhuepf.bsky.social, Christian Tischer, Pete Bankhead, @kbias.bsky.social @bethcimini.bsky.social My Fiji training notes are now FAIR. All online in an open format to download and use for teaching and training. All in Google Doc or PDF formats bit.ly/4hkfEBF

I put together a small guide on how to get started with Fiji. Please distribute to anyone who might benefit form this! zenodo.org/records/1477... #imageanalysis #fiji #imagej #training

We CT scanned thousands of vertebrates from US natural history collections and made them freely available. Countless people have used the data for research (>200 pubs) and to learn anatomy/morphology. www.morphosource.org/projects/000...

🚨Important service release announcement A new BoneJ (7.0.20) is available that keeps up with changes in ImageJ (specifically, the move to scijava 40.0.0). Just let the updater run.

My lab has a tradition that each week one person contributes edits to a Wikipedia page relevant to their scientific work, and then presents it briefly at lab meeting (and we clap). A few of my favorites: en.wikipedia.org/wiki/Proprio... en.wikipedia.org/wiki/Chionea en.wikipedia.org/wiki/Femoral...

There's a new wave of discussion to improve the clarity of Fiji's original menus and plugins. If you have opinions or suggestions to make, don't hesitate to participate on the forum! forum.image.sc/t/houseclean... #microscopy #imagej #fiji