BoneJ
Scientific software for bone image analysis.
- 📢 Release alert! This one lets *all* Intel GPUs use BoneJ+ 🤖 If you have an Intel Iris Xe, UHD or Arc, support is more robust. Background: Intel omitted 64-bit floating point precision (double) in their GPUs since c. 2020: this update uses the universally-supported single-precision float type.
- 📢 New release! This one makes BoneJ's GPU-accelerated extensions easier to access from Python by using ImageJ2 / scijava-style wrappers. Just let the Fiji updater run and grab a voucher from bonej.org/shop
- Reposted by BoneJJoin me for a tutorial on @bonej.org 17 November 13h00 CET
- 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.
- Analysis of 985(!!) baboon skulls' CT scan data from MorphoSource shows that >18% have slice spacing errors that propagate to downstream analyses-- an important cautionary tale on checking CT metadata vs. errors, and a goliath effort: peerj.com/articles/201...
- A closer read of this paper makes it seem that some of the scans were done in chunks of a few slices each, and that the chunks had different slice spacing from each other. That's a bit of a mess: making a composite assuming equal z-spacing throughout the volume will lead to distortions.
- Could be fixed by determining the total number of slices and start and end slice position, then calculating average slice spacing and interpolating the original image data accordingly. A bit messy. Good on 3D Slicer for detecting, alerting users and sorting it!
- Reposted by BoneJImageJ/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.
- Analysis of 985(!!) baboon skulls' CT scan data from MorphoSource shows that >18% have slice spacing errors that propagate to downstream analyses-- an important cautionary tale on checking CT metadata vs. errors, and a goliath effort: peerj.com/articles/201...
- Reposted by BoneJIt 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
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- Analysis of 985(!!) baboon skulls' CT scan data from MorphoSource shows that >18% have slice spacing errors that propagate to downstream analyses-- an important cautionary tale on checking CT metadata vs. errors, and a goliath effort: peerj.com/articles/201...
- Reposted by BoneJWant 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...
- Reposted by BoneJGotta 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.
- Reposted by BoneJDo 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.
- Reposted by BoneJ📣 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...
- Reposted by BoneJBioImage 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!
- Reposted by BoneJCome 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 🤞
- Reposted by BoneJWant 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!
- Reposted by BoneJImages 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!
- 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...
- 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...
- 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.
- Reposted by BoneJI 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 bonej@bonej.org to get a coupon for a 100% discount on your first token.
- 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 bonej@bonej.org if you'd like a free coupon to try it out!
- 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.
- Reposted by BoneJ🦴 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...
- Reposted by BoneJ[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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- Finally made it to the @mnhn.fr! The vertebrate skeleton is just so stunning in all its variety, this place showcases it like no other.
- Reposted by BoneJWorking 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...
- Reposted by BoneJRegister 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
- Reposted by BoneJ📢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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- Reposted by BoneJI 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?)
- Reposted by BoneJ☀️ 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
- Reposted by BoneJAmazing 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-...
- Reposted by BoneJThe 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...
- Reposted by BoneJI 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
- Reposted by BoneJMain 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 🦖🇿🇼🦕
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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 - Reposted by BoneJI 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
- Reposted by BoneJWe 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.
- Reposted by BoneJMy 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...
- Reposted by BoneJThere'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
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- Getting closer to releasing first versions of BoneJ+, which brings GPU acceleration and improved precision. Ellipsoid Factor is first up, and nearly ready! Give us a shout if you'd like to be an alpha tester 🤓
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- Stay tuned for GPU-accelerated and more accurate Ellipsoid Factor in my upcoming Plus release! Ellipsoid Factor was a key metric to define the unusual morphology of the helmeted hornbill's casque trabecular bone, which is much more rod-like than expected.
- 🚨 New paper on helmeted hornbill trabecular bone with Hong Kong colleagues. The bone in the casque is remarkable - my eye was first caught by a specimen in the @nhm-london.bsky.social. Trabeculae are arranged unusually like a bundle of long, thick sticks melted together. doi.org/10.1111/nyas...
- Reposted by BoneJ📣 Many #EuroBioImaging Nodes, facilities & friends are on BlueSky🦋! Here are some to follow 🔽 @bioimaginguk.bsky.social @france-bioimaging.bsky.social @danishbioimaging.bsky.social @sln-icfo.bsky.social Don't miss the starter pack 🔽 go.bsky.app/VoeAfuN Join us - Nominate yourself or reply here!at://did:plc:rtm3mo4ssfozn3wtasr5sc4c/app.bsky.graph.starterpack/3lb6c3hsf6f2h
- Reposted by BoneJDouble Job Alert!! We are recruiting an archaeobotany technician and an osteology (human & zooarchaeology) technician to help curate and improve access to our collections. Come join us at the Institute for Archaeology, University College London www.ucl.ac.uk/archaeology/...
- Reposted by BoneJThanks for the endorsement! @bonej.org is here on bsky 🦋
- I like mvn and JUnit because they keep me in one piece...
