iiinova — where your digital self keeps evolving

BoneJ @bonej.org · 11/09/2026

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.

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Virginie Uhlmann @virginieuhlmann.bsky.social · 11/09/2026

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.

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Institute for Research Software @softwaresaved.bsky.social · 25/08/2026

🎉 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...

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BoneJ @bonej.org · 27/08/2026

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

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BoneJ @bonej.org · 25/07/2026

📢 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.

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Michael Doube @mdoube.bsky.social · 18/06/2026

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.

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BoneJ @bonej.org · 13/06/2026

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

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BoneJ @bonej.org · 12/06/2026

📢 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

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BoneJ @bonej.org · 10/06/2026

📢 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.

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AltYellostoneNatPar @altyellonatpark.org · 08/06/2026

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

Mamma moose and calf in a field of willow.

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Daniel Gorelick @danielgorelick.bsky.social · 03/06/2026

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...

Scatter plot showing that Fast & Fair peer review reached first decision with reviews much faster than conventional peer review: mean 5.5 versus 37.7 working days. Most Fast & Fair manuscripts met the 7-working-day target, while conventional manuscripts were slower and more variable, up to 116 working days.

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Joel Lüthi @joelluethi.bsky.social · 01/06/2026

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

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Virginie Uhlmann @virginieuhlmann.bsky.social · 01/06/2026

📢📢 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...

jobs.uzh.ch

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...

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Professor John R. Hutchinson @johnrhutchinson.bsky.social · 27/05/2026

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.

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Michael Doube @mdoube.bsky.social · 13/05/2026

@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...

doi.org

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...

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SWC/GCNU Neuroinformatics Unit @neuroinformatics.dev · 13/03/2026

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

neuroinformatics.dev

Get involved — NIU

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Michael Doube @mdoube.bsky.social · 11/03/2026

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

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Michael Doube @mdoube.bsky.social · 11/03/2026

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

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Michael Doube @mdoube.bsky.social · 05/03/2026

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

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BoneJ @bonej.org · 05/03/2026

📢 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.

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Methods in Ecology and Evolution @methodsinecoevol.bsky.social · 22/02/2026

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

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BoneJ @bonej.org · 07/01/2026

📢 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.

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BoneJ @bonej.org · 27/11/2025

📢 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

bonej.org

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Michael Doube @mdoube.bsky.social · 03/11/2025

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

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Michael Doube @mdoube.bsky.social · 27/10/2025

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.

github.com

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Michael Doube @mdoube.bsky.social · 27/10/2025

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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BoneJ @bonej.org · 27/10/2025

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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Dave Barry @david-j-barry.bsky.social · 23/10/2025

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...

imagej.github.io

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...

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Michael Doube @mdoube.bsky.social · 13/10/2025

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.

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BoneJ @bonej.org · 13/10/2025

📢 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.

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Jean-Yves Tinevez @jytinevez.bsky.social · 03/10/2025

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

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BoneJ @bonej.org · 02/10/2025

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

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Ignacio Arganda-Carreras @iarganda.eurosky.social · 30/09/2025

📣 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...

cvpd.github.io

📢 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...

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Siân Culley @superresolusian.bsky.social · 29/09/2025

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-...

kcl.ac.uk

Bioimage Analysis Specialist | King's College London

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BoneJ @bonej.org · 25/09/2025

🦴 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 · 19/09/2025

So bad it's good Rrrr we love the Ccc

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BoneJ @bonej.org · 16/09/2025

📢 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 · 16/09/2025

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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Guillaume Jacquemet @guijacquemet.bsky.social · 10/09/2025

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...

abo.rekrytointi.com

University Researcher in Bioimaging / Universitetsforskare med inriktning bioimaging, 1.11.2025-31.12.2030

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BoneJ @bonej.org · 12/09/2025

🔥🔥🔥 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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The Francis Crick Institute @crick.ac.uk · 12/09/2025

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...

crick.ac.uk

CBIAS napari workshop 2025

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BoneJ @bonej.org · 06/09/2025

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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Horizons Magazine @horizons-en.bsky.social · 05/09/2025

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

horizons-mag.ch

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BoneJ @bonej.org · 02/09/2025

📢 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 · 31/08/2025

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.

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BoneJ @bonej.org · 30/08/2025

😮 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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AltYellostoneNatPar @altyellonatpark.org · 30/08/2025

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

gofund.me

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

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