Reposted by Michael DoubeBoneJ @bonej.org · 23hYour 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." 022
Michael Doube @mdoube.bsky.social · 05/10/2026It doesn't get much better than this - great boss, great location, great work. Apply! 020
Reposted by Michael DoubeDale Moulding @dalemoulding.bsky.social · 01/10/2026Having seen the news: www.bbc.co.uk/news/article... thought I'd share a cilia movie captured at UCL GOS ICH with Eriomina Shahaj & Vanesa Papastavrou using simple DIC on a Nikon Ti2 with DIC at 60x1.4. 500 fps here slowed down 20 times. Processed with Nikon's denoiseAI and an unsharp mask in Fiji. 88722
Michael Doube @mdoube.bsky.social · 01/10/2026Clinicians includes vets - and looks like it is internationally open as well. 010
Reposted by Michael DoubeBiology Open @biologyopen.bsky.social · 01/10/2026In guinea fowl, walking and running form a continuum of center-of-mass dynamics in which the rotation sense of the velocity loop indicates the walk-run divide. Read the article by Monica A. Daley and Aleksandra Birn-Jeffery doi.org/10.1242/bio.... 101
Michael Doube @mdoube.bsky.social · 01/10/2026For NVIDIA and AMD testing I have a couple of Thunderbolt attached GPUs. The AMD one is a dedicated eGPU, while the NVIDIA one is mounted to a workstation power supply on a "Shenzhen Special" weird little dock thing. With these devices I can quickly check that the OpenCL code is portable. 000
Michael Doube @mdoube.bsky.social · 01/10/2026The Iris Xe is in a Windows laptop, where I have BoneJ set up in an XamFlow workflow. 100
Michael Doube @mdoube.bsky.social · 01/10/2026Getting income from @beancounter.ch means in practice that @bonej.org continues to improve and stays relevant in a changing world, because it's worth my time to continue working on it. 000
Michael Doube @mdoube.bsky.social · 01/10/2026Intel GPUs like the ones commonly found in Windows and Linux laptops. I am developing on a c. 2017 HD Graphics 515 in Ubuntu and testing on a c. 2021 Iris Xe 110
Michael Doube @mdoube.bsky.social · 01/10/2026All these posts about the cool screenings at @princecharlescinema.com almost make me want to move back to London. 010
Reposted by Michael DoubeUK-BIAS @uk-bias.bsky.social · 17/09/2026Drowning in Image data? Know there’s a better way to analyse it, but don’t know where to start? 📣 UK-BIAS to the rescue! 👩💻🧑💻👨💻We’re the first dedicated #BioImageAnalysis service in the UK-node of @eurobioimaging.bsky.social bringing together specialists from ten UK institutions. 👩💻🧑💻👨💻 11211
Michael Doube @mdoube.bsky.social · 28/09/2026@nature.com has an obvious conflict of interest in running this story. They benefit from a huge amount of reviewing labour that others pay for. Reminder: @springernature.com is half owned by one person. Why are you NOT insisting that he pay for your expert opinion, like any other professional? 010
Reposted by Michael DoubeOsteoarthritis and Cartilage Journal @oacjournal.bsky.social · 28/09/2026New in #OAC! Phase-contrast synchrotron microtomography of human articular #cartilage samples reveal age-related changes with similar fidelity as histology, while providing substantial additional quantitative information. Read more: sciencedirect.com/science/arti... 002
Reposted by Michael DoubeBeanCounter.ch @beancounter.ch · 28/09/2026Thanks to scyjava, BeanCounter.ch vouchers are trivial to integrate into Python projects. Coming soon - @napari.org plugins! Drop us a line if you're interested to join as an affiliate and get paid when your plugins are used. 002
Reposted by Michael Doubenapari @napari.fosstodon.org.ap.brid.gy · 26/09/2026🚀 napari is hiring Remote Developers-in-Residence! Join us to build the future of interactive n-dimensional data visualization in Python. 💻 60% Dev / 20% Maintenance / 20% Community & Outreach 💰 $59.50/hr (Contract, 14–35 hrs/wk) 🌍 100% Remote, open globally Learn more and apply today […]fosstodon.orgOriginal post on fosstodon.org 0911
Michael Doube @mdoube.bsky.social · 25/09/2026Normally I avoid social media outrage - switch off, block, etc. But there's a sprouting of a special kind. Real microscopic imaging vs. fabrication of epithelial cilia. Fabulous. Everyone who's in love ❤️ with ML inference 🤖: it's not measurement data. It's just filling the gaps with a guess. 000
Michael Doube @mdoube.bsky.social · 23/09/2026But maybe it's the natural extension of using inference as though it is measurement. A cautionary tale for our time. 001
Michael Doube @mdoube.bsky.social · 18/09/2026OK - but what I actually want to do is see if I can get @beancounter.ch (in Java, using SciJava Commands) to play nicely with Python clients. ] pip install scyjava ] python3 beancounter_example.py OMG it works... 000
Michael Doube @mdoube.bsky.social · 18/09/2026Napari does in fact have downloads for regular users: napari.org/stable/getti... But that would be a bit easy, right? And a lot of my interest is in developing with / for it.napari.orgInstall napariInstall with Python Install napari in a Python environment for the most customizable experience. Install as Python package Download napari app A standalone installer for when you want napari without s... 000
Michael Doube @mdoube.bsky.social · 18/09/2026Then when it's done you just run napari to get a GUI ] napari Easy when you know how. Good that Proton's Lumo chatbot could make sense of the process because it would have otherwise been very very frustrating. (and I'm no newbie). 100
Michael Doube @mdoube.bsky.social · 18/09/2026Then you go into the conda environment ] conda activate napari-stable and get all the Napari stuff ] pip install "napari[all]" pip does the same job as apt - gets all the libraries and makes sure they all say they are going to play well together. 100
Michael Doube @mdoube.bsky.social · 18/09/2026If I understand it correctly, each environment is a whole fresh and huge set of libraries with compatible versions, which you have to do because otherwise nothing works. ] conda create -n napari-stable python=3.11 -y Also the Python version is super critical, down to 2 DP. 100
Michael Doube @mdoube.bsky.social · 18/09/2026First you need an environment that sits behind / beside your CLI - this means layer upon layer of massive quantities of bloat if you go for the full Monty Conda installation (9.8 GB!). Miniconda is smaller though. ] chmod +x Miniconda3-latest-Linux-x86_64.sh ] ./Miniconda3-latest-Linux-x86_64.sh 100
Michael Doube @mdoube.bsky.social · 18/09/2026But - it's not so straightforward to just download and go in Python land. Pity the poor regular users who just want to do a thing in a GUI. I have at least the advantage of 25+ years using Linux, command line stuff is normal and even comfortable. 200
Michael Doube @mdoube.bsky.social · 18/09/2026The good news is that these days we have LLMs which have scraped all your code and can write the documentation that you haven't (or one hasn't, mea culpa). So to begin: I heard a lot about @napari.org and thought I probably should at least take a look... 101
Michael Doube @mdoube.bsky.social · 18/09/2026Starting a chronicle here, mostly for my own reference and maybe others' entertainment, of my battles in Python land. Python, I've heard, is quite popular despite being really slow and a bugger to get to work and keep straight on your system. In fact, some of my best friends are Python developers. 110
Reposted by Michael DoubeCNRS @cnrs.fr · 15/09/2026Researchers have sorted out and deciphered thousands of letters written in cuneiform script on clay tablets found in Mesopotamia. 📜 These are eerily modern, showing that people four millennia ago shared the same interests and concerns as we do todaynews.cnrs.frLive from Mesopotamia, 4,000 years ago 34422
Reposted by Michael Doubepaveltomancak.bsky.social @paveltomancak.bsky.social · 10/09/2026This article seems to celebrate the shift from poor support for #software #engineers in research to pretending they aren't needed at all. Did we spend 2 decades consolidating fragmented software ecosystems into platforms only to see them dissolve through "vibe coding"? www.nature.com/articles/s41...nature.comDisruption of the research software landscape through AI software generation - Nature MethodsSpecialized research software has historically been costly and time-consuming to create, but large language models (LLMs) have become capable enough at code generation to fundamentally change this. We... 7309
Reposted by Michael DoubeRoyal Society Publishing @royalsocietypublishing.org · 08/09/2026Interested in joining the #RSOS editorial board? We seek enthusiastic & engaged Associate Editors who will perform a range of valuable tasks for the journal and the communities it serves. The application deadline is 30 October 2026. Find out more: royalsocietypublishing.org/rsos/pages/e... 064
Reposted by Michael DoubeMichael Doube @mdoube.bsky.social · 11/03/2026How 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 013
Reposted by Michael DoubeBeanCounter.ch @beancounter.ch · 08/09/2026📢 Just added: a special voucher type for developer affiliates to use in their CI/CD pipelines. Drop us a PM if you'd like to join as an affiliate and start getting paid (in real money 💶, not crypto, Brownie points, warm fuzzies or good vibes) when people use your software. 002
Reposted by Michael DoubeInstitute for Research Software @softwaresaved.bsky.social · 01/09/2026⬡ Today, we become the Institute for Research Software. For 15 years, we've worked as the Software Sustainability Institute to make research software more sustainable and properly recognised. 13325
Reposted by Michael DoubeSophie Regnault @sesamoidstreet.bsky.social · 01/09/20261 year teaching post in anatomy/physiology in beautiful West Wales. Closes Sunday! Please share widely jobs.aber.ac.uk/en/vacancy/v... 001
Reposted by Michael DoubeInstitute 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... 036
Reposted by Michael DoubeLe Monde @lemonde.fr · 30/08/2026A l’approche de l’hiver, le crâne des musaraignes s’aplatit, tandis que leur museau s’élargitlemonde.frA l’approche de l’hiver, le crâne des musaraignes s’aplatit, tandis que leur museau s’élargitLe phénomène, observé chez une espèce japonaise, pourrait être une adaptation à la raréfaction de la nourriture et au froid. L’anatomie changeante de ce petit mammifère intrigue les chercheurs. 23311
Reposted by Michael DoubeBeanCounter.ch @beancounter.ch · 27/08/2026Looking 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 011
Reposted by Michael Doubeploum @ploum.mamot.fr.ap.brid.gy · 09/08/2026En 2006, il était presqu’obligatoire de payer un logiciel Microsoft pour avoir le droit d’utiliser un ordinateur. Et je trouvais ça injuste… En 2026, il est presqu’obligatoire d’avoir un compte chez Google et chez Meta qui nous espionne en permanence juste pour avoir le droit de vivre… 144
Reposted by Michael DoubeCommon Tern Project @commonternproject.bsky.social · 10/08/2026Question: do I know anyone near Nantes who would be willing to pick up a dead gull-billed tern and its logger? L49 has sadly been killed near a road. I’d be very grateful for a picture and the logger and would of course reimburse postage. 553100
Reposted by Michael DoubeBoneJ @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. 002
Michael Doube @mdoube.bsky.social · 04/07/2026Pleased to report that I have been paid in cold hard pounds sterling for a Fast and Fair review job. Just like when I was in the clinic: payment for professional advice. Money has a purpose and this is it. Better than vouchers, crypto or Brownie points because I can do what I want with it. 000
Michael Doube @mdoube.bsky.social · 03/07/2026Maybe git needs a new term here, like "code produced by" or "generated by" to strip out the personhood that's implied by "author". The LLMs all use friendly "I" "am" "thinking" user feedback when they are processing requests, but they aren't "I" and they definitely aren't thinking. 000
Reposted by Michael DoubeClimate.us @climate.us · 23/06/2026Check out New York Times coverage of our full website launch! www.nytimes.com/2026/06/23/c... 5226100
Reposted by Michael DoubeMichael Doube @mdoube.bsky.social · 11/05/2026Looking forward to returning to my PhD alma mater @qmul.bsky.social this July for back-to-back ISBM and BRS meetings: www.bonemorphometry.org/isbm-2026/ boneresearchsociety.org/meeting/brs2... See you there! 011
Michael Doube @mdoube.bsky.social · 18/06/2026Just 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. 121
Reposted by Michael DoubeBoneJ @bonej.org · 13/06/2026Interested in trying BoneJ+ with accelerated GPU processing? Drop us a DM to get a free @beancounter.ch voucher to try it out! 002
Reposted by Michael DoubeBoneJ @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 002
Reposted by Michael DoubeMadeleen Brink @madeleenbrink.bsky.social · 09/06/2026Based in Ireland and work with imaging? @microscopyirl.bsky.social & Core Facilities Network Ireland are making the case to government for an Irish @eurobioimaging.bsky.social node. Take our short survey by June 25th docs.google.com/forms/d/e/1F... Please RT! 🙏 #Microscopy #Bioimagingdocs.google.comMicroscopy Ireland Irish Imaging Community SurveySupporting the case for an Irish Euro-BioImaging Node Prepared by Microscopy Ireland (MSI) and the National Core Facilities Network 035
Reposted by Michael DoubeBoneJ @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. 012
Reposted by Michael DoubeSICB journals @sicbjournals.bsky.social · 09/06/2026IOB "This study applies #biomaterials/imaging techniques to #wildlife forensics, using micro-computed #tomography to forensically analyse bullet-induced damage in a unique collection of helmeted hornbill skull specimens..." doi.org/10.1093/iob/... Chan et al #birds #biology #organisms 021
