🎉 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!

BeanCounter.ch@beancounter.ch · last wk.

Looking for an all-you-can-eat software buffet? Introducing BeanCounter Unlimited! Subscriptions available in one month, three month and one year durations, now from beancounter.ch/unlimited

📢 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!

Virginie Uhlmann@virginieuhlmann.bsky.social · 3mo ago

📢📢 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...

📢📢 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...

UZH: Bioimage Analyst

The University of Zurich is the largest university in Switzerland and one of the most prominent in Europe. For research purposes the Biovision Center and Flow Cytometry Facility offer services to supp...

jobs.uzh.ch

I've been to 3, maybe 4 London high profile expert lectures/discussions on AI in science since 2025 and not one has mentioned the negative environmental impacts such as climate change and water usage or societal impacts such as IP theft, privacy violation & job loss. It is deeply worrying.

@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...

Cooling History of Chang'e‐5 Basalts Recorded by Diffusion‐Driven Mg and Fe Isotope Fractionation

Remarkable and negatively correlated δ26Mg and δ56Fe variability at the mineral scale is observed in a Chang'e-5 basalt clast Chemical diffusion in mineral grains within a cooling melt caused the...

doi.org

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.

BoneJ@bonej.org · 6mo ago

📢 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.

📢 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

Beth Cimini 🔬💻📊@bethcimini.bsky.social · 10mo ago

Do you want to learn more about 25+ bioimage analysis tools, 100% for free? Sign up to attend Halfway to I2K today! tinyurl.com/Halfway-to-I... Wishing you'd submitted a tool or workshop but missed the deadline? GREAT NEWS, we just extended one week! Submit by Friday - airtable.com/app2zpB8d82r...

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.

Professor John R. Hutchinson@johnrhutchinson.bsky.social · 10mo ago

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...

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

BoneJ@bonej.org · 10mo ago

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.

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.

Professor John R. Hutchinson@johnrhutchinson.bsky.social · 10mo ago

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...

👀

Professor John R. Hutchinson@johnrhutchinson.bsky.social · 10mo ago

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...

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...

Batch Processing with the ImageJ Macro Language

The ImageJ wiki is a community-edited knowledge base on topics relating to ImageJ, a public domain program for processing and analyzing scientific images, and its ecosystem of derivatives and variants...

imagej.github.io

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 · 11mo ago

📢 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!!

Michalis Averof@michalis-averof.bsky.social · 11mo ago

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