BoneJ

📢 Out Now in BoneJ+: Improved 3D skeletonisation performance, on Intel GPUs. Compiler optimisation is back on, giving 🔥 10× 🔥 speedup. Special mention to Windows, whose flakiness exposed buggy behaviour of the unoptimised OpenCL kernel. You *might* have to update your graphics driver 🤷‍♂️

An unsung #Czech hero who saved the Internet yesterday. Excerpt: "When I started doing open-source, it was fun. And it kind of still is. But the environment has shifted. Open-source sometimes feels like exploitation."

We completed the publication project "Focus on the methods reproducibility of bioimage analysis", started in #GloBIAS 2024. Here is the editorial for the special issue of the Journal of Microscopy explaining the aim of this action (open access). onlinelibrary.wiley.com/doi/10.1111/...

Your periodic reminder that freedom isn't free. "While essential for getting started, grant support is not a sustainable long term solution for funding daily operations."

Get in touch to learn more about BoneJ × XamFlow

BoneJ+ development is supported by @beancounter.ch , a new voucher scheme that connects software users and developers.

Drop us a line to get a free trial voucher to try BoneJ+! beancounter.ch/shop

LLMs have helped speed up and improve the quality of engineering new features and fixing bugs. For us, they're power tools that help skilled people work more effectively - in the same way that circular saws, nail guns and CNC machines help properly trained people build things in the physical world.

Research software is costly and time-consuming to produce because it requires focused time from developers who have invested years learning to master their craft, just like art. There is nothing to celebrate about relinquishing intellectual expertise and mastery in favor of fast and cheap.

🎉 Big news is coming. Next week we'll unveil a new name and brand identity for the Software Sustainability Institute that captures the work we do today, honours what we've achieved so far, and sets the stage for what's next. Watch this space 👀 www.software.ac.uk/blog/new-ide...

Use as much BoneJ+ as you want with a subscription voucher!

📢 Release alert! BoneJ+ is now callable in headless mode, including specifying which GPU(s) to use. ~/Fiji/fiji --headless -Dbonej.plus.devices="1-0" --run run_all_bonej_plus.py Drop us a line if you'd like to know more and to get a demo script.

Just merged a pull request from @ctrue.bsky.social into @bonej.org 's master branch solving a long-standing CI annoyance (🙏). Weirdly, Anthropic's Claude LLM has inserted text claiming that it is a co-author. One should use the best tools for the job (e.g. IDEs), but tools are not authors.

Interested in trying BoneJ+ with accelerated GPU processing? Drop us a DM to get a free @beancounter.ch voucher to try it out!

📢 Release alert! BoneJ+ 0.0.20 brings stability to GPU checking on Windows and belatedly bumps the minimum Java version to 17. Check it out! Drop us a DM to get a tester voucher from @beancounter.ch

📢 Release alert! radius-r0 uses Scijava Datasets as the image format for input-output, and harmonises all the plugins to use the same results table. Scripting users will need to update their scripts to use Dataset and SharedTable; internally, functionality is the same.

We study papillomavirus in moose and how they shed the disease with no scarring and no adverse effects on their reproductive capabilities, hoping their solution is applicable in human medicine. We do the field work and provide the data. We can't do it without you. Please donate tonight

Paying peer reviewers works. Expanded Fast & Fair experiment @biologyopen.bsky.social: • 5.5 vs 37.7 working days to decision with reviews • ~3 vs ~9 reviewer invitations per manuscript • no reduction in editor-assessed review quality • similar acceptance rates www.biorxiv.org/content/10.6...

Want to work with us at the BioVisionCenter on building new cool OME-Zarr image analysis workflows? Apply to our Bioimage Analyst position!

📢📢 We are hiring a Bioimage Analyst at the BioVisionCenter! 📢📢 Join our collaboration with the Flow Cytometry Facility and contribute back to the international efforts on open standards for bioimaging data! More information here, reach out if you have any question: jobs.uzh.ch/job-vacancie...

@bonej.org has been supporting the bone research community for over 15 years. Ever since the early days of the project, there have been lots of other uses. Check out this paper that used BoneJ for measuring basalt rock formation on the Moon 🌕, from the Chang'e-5 mission! doi.org/10.1029/2025...

We have three neuroscience research software engineering jobs available at @sainsburywellcome.bsky.social, two joint with the Advanced Microscopy Facility. All positions start ASAP, funded until Sept 2028 in the first instance. Salary £54-64k. More details: neuroinformatics.dev/get-involved

Weird when your "hobby" can be used by others for their profit. The traditional way to receive thanks for doing work that has value to others is to take payment 💰. I've been working on a mechanism to do this, currently working for BoneJ+, and easy to set up for other ImageJ plugins @beancounter.ch

How can we make sure community software projects that are delivering value are worth looking after from the developers' perspective? I've always found that being paid is highly motivating. Now there is a fair way for users to help developers keep going: @beancounter.ch

Taking (paid) requests to make enhancements to @bonej.org. What would make it better for you? Contact me for a quote.

📢 Release alert! BoneJ ulna-r10 brings much anticipated ROI support to Area/Volume Fraction. TV (TA) = pixel volume (area) in the ROI BV (BA) = foreground pixel volume (area) in the ROI Thanks to Sandra Shefelbine at Northeastern for commissioning development of this much-requested enhancement.

The deadline for applying to be an Associate Editor has been extended to the 8th March! MEE are looking for expertise across a range of topics, including stable isotopes, ecophysiology, mark-recapture methods and modelling, and more! Find out more and apply here 👇 buff.ly/MzIXj6U

📢 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

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

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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.

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.