Pinned
Michael Doube
@mdoube.bsky.social
· Oct 13
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.
Drop me a PM to get a token to try it out for free.
One of the "exciting" things about GPU development is all the funny quirks that hardware vendors come up with that keep life interesting. Wrt. OpenCL support AMD is the most compliant and predictable; NVIDIA is mostly OK but a bit odd sometimes; Intel lacks useful things for science like FP64.
📢 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.
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.
January 7, 2026 at 8:01 PM
One of the "exciting" things about GPU development is all the funny quirks that hardware vendors come up with that keep life interesting. Wrt. OpenCL support AMD is the most compliant and predictable; NVIDIA is mostly OK but a bit odd sometimes; Intel lacks useful things for science like FP64.
Reposted by Michael Doube
Swiss Breeding Bird Monitoring dataset is now openly accessible! The team from @vogelwarte.bsky.social made the long-term dataset of the Swiss CBM program (“Monitoring Häufige Brutvögel”, MHB) freely available under CC-BY 4.0 licence. esajournals.onlinelibrary.wiley.com/doi/10.1002/...
December 30, 2025 at 6:03 PM
Swiss Breeding Bird Monitoring dataset is now openly accessible! The team from @vogelwarte.bsky.social made the long-term dataset of the Swiss CBM program (“Monitoring Häufige Brutvögel”, MHB) freely available under CC-BY 4.0 licence. esajournals.onlinelibrary.wiley.com/doi/10.1002/...
Reposted by Michael Doube
The banality of evil.
“Like Prime, but with human beings.”
December 26, 2025 at 5:31 AM
The banality of evil.
Reposted by Michael Doube
Attending #CellBio2025? Have questions about publishing with Biology Open @biologyopen.bsky.social or our Fast & Fair peer review initiative? Meet Editor-in-Chief @danielgorelick.bsky.social on Tuesday, 9 December, 12:00 -13:00 pm at booth 1232.
December 8, 2025 at 3:04 PM
Attending #CellBio2025? Have questions about publishing with Biology Open @biologyopen.bsky.social or our Fast & Fair peer review initiative? Meet Editor-in-Chief @danielgorelick.bsky.social on Tuesday, 9 December, 12:00 -13:00 pm at booth 1232.
The licence you put on your work needs to sustain your ability to continue it. Otherwise it's self-defeating and you'll be taken advantage of.
RE: https://writing.exchange/@erlend/115549403577231766
I've been thinking over and over this article. Like many advocates of free culture, my first instinct is the dogmatic reaction that "open" must be open to all (a dogma that took hold in the 90s-00s). The article points out (among many […]
I've been thinking over and over this article. Like many advocates of free culture, my first instinct is the dogmatic reaction that "open" must be open to all (a dogma that took hold in the 90s-00s). The article points out (among many […]
Original post on mastodon.social
mastodon.social
December 8, 2025 at 6:46 AM
The licence you put on your work needs to sustain your ability to continue it. Otherwise it's self-defeating and you'll be taken advantage of.
Reposted by Michael Doube
Final pdf is out! journals.biologists.com/jeb/article/...
December 1, 2025 at 6:50 AM
Final pdf is out! journals.biologists.com/jeb/article/...
Reposted by Michael Doube
Do you have 2D-to-3D image registration challenges? Let me know about them here
forum.image.sc/t/toward-bet...
forum.image.sc/t/toward-bet...
Toward better 2D - 3D registration in BigWarp
BigWarp has so far focused on 2D-2D or 3D-3D registration, and not on 2D-3D registration. After a conversation with @Christian_Tischer , we thought some simple UI changes could make the support for 2...
forum.image.sc
November 29, 2025 at 6:03 PM
Do you have 2D-to-3D image registration challenges? Let me know about them here
forum.image.sc/t/toward-bet...
forum.image.sc/t/toward-bet...
Reposted by Michael Doube
📢 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
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
bonej.org
November 27, 2025 at 7:29 PM
📢 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
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 Michael Doube
November 25, 2025 at 1:06 PM
Looking forward to catch up with @cbias.bsky.social next week, and reconnect with the old London crew. See you there!
tidal.com/playlist/d9d...
tidal.com/playlist/d9d...
London 🇬🇧
Playlist - London 🇬🇧 - 37 items
tidal.com
November 22, 2025 at 10:56 AM
Looking forward to catch up with @cbias.bsky.social next week, and reconnect with the old London crew. See you there!
tidal.com/playlist/d9d...
tidal.com/playlist/d9d...
Reposted by Michael Doube
We just released a new major version of TrackMate (v8), the cell and organelle tracking plugin of Fiji.
It ships many new features, detailed below, but that are articulated around the following:
It ships many new features, detailed below, but that are articulated around the following:
November 20, 2025 at 11:42 AM
We just released a new major version of TrackMate (v8), the cell and organelle tracking plugin of Fiji.
It ships many new features, detailed below, but that are articulated around the following:
It ships many new features, detailed below, but that are articulated around the following:
Reposted by Michael Doube
We're pleased to announce that our latest release of new and updated UK Biobank data is now available to approved researchers around the world ✅
November 20, 2025 at 9:09 AM
We're pleased to announce that our latest release of new and updated UK Biobank data is now available to approved researchers around the world ✅
Reposted by Michael Doube
Python notebook from a two year old paper:
Oh, no, I cannot run, there is a slight mismatch of a logging library.
ImageJ plugin from 2001 running on Quantum Java 51 in 2078:
Your 100 petabyte temporal hologram was successfully thresholded.
Oh, no, I cannot run, there is a slight mismatch of a logging library.
ImageJ plugin from 2001 running on Quantum Java 51 in 2078:
Your 100 petabyte temporal hologram was successfully thresholded.
November 20, 2025 at 5:42 PM
Python notebook from a two year old paper:
Oh, no, I cannot run, there is a slight mismatch of a logging library.
ImageJ plugin from 2001 running on Quantum Java 51 in 2078:
Your 100 petabyte temporal hologram was successfully thresholded.
Oh, no, I cannot run, there is a slight mismatch of a logging library.
ImageJ plugin from 2001 running on Quantum Java 51 in 2078:
Your 100 petabyte temporal hologram was successfully thresholded.
Reposted by Michael Doube
When you think of bats, you probably don’t think of pollination - but bats are crucial pollinators, and the key to creating a certain drink! 🍸
See an (adorable) bat covered in pollen and learn why a world without bats would be a world without tequila in this week’s Surprising Science. 🦇
See an (adorable) bat covered in pollen and learn why a world without bats would be a world without tequila in this week’s Surprising Science. 🦇
November 17, 2025 at 3:09 PM
When you think of bats, you probably don’t think of pollination - but bats are crucial pollinators, and the key to creating a certain drink! 🍸
See an (adorable) bat covered in pollen and learn why a world without bats would be a world without tequila in this week’s Surprising Science. 🦇
See an (adorable) bat covered in pollen and learn why a world without bats would be a world without tequila in this week’s Surprising Science. 🦇
Reposted by Michael Doube
Philippe Taquet, chasseur de dinosaures et ancien directeur du Muséum national d’histoire naturelle, est mort
Philippe Taquet, chasseur de dinosaures et ancien directeur du Muséum national d’histoire naturelle, est mort
Destiné à reprendre l’industrie textile familiale, cet esprit libre a préféré la vie de chercheur d’os, découvrant plusieurs espèces d’animaux disparus, tout en menant une carrière institutionnelle de premier plan. Il s’est éteint le 16 novembre, à 85 ans.
www.lemonde.fr
November 17, 2025 at 10:55 AM
Philippe Taquet, chasseur de dinosaures et ancien directeur du Muséum national d’histoire naturelle, est mort
Reposted by Michael Doube
If you're interested in developing an open-source image analysis platform/plugin to profile bacteria with deep learning while living in the beautiful city of Paris 🇫🇷, check out this job ad from the @chzimmer.bsky.social lab @pasteur.fr
research.pasteur.fr/fr/job/open-...
research.pasteur.fr/fr/job/open-...
Open-Source Developer for Deep Learning Antibiotic Discovery Platform - Research
Introduction Antimicrobial resistance (AMR) is one of the most urgent global health threats projected to cause up to 10 million deaths per year by 2050. The AI4AMR project brings together teams from I...
research.pasteur.fr
November 15, 2025 at 9:22 AM
If you're interested in developing an open-source image analysis platform/plugin to profile bacteria with deep learning while living in the beautiful city of Paris 🇫🇷, check out this job ad from the @chzimmer.bsky.social lab @pasteur.fr
research.pasteur.fr/fr/job/open-...
research.pasteur.fr/fr/job/open-...
Reposted by Michael Doube
Remember that survey about how we can sustain napari development? We extended the deadline until the 16th, AoE! Blog post: napari.org/island-dispa...
Survey: napari.typeform.com/sustainability
If you use napari at all we would be super grateful if you filled it in! 🙏
Survey: napari.typeform.com/sustainability
If you use napari at all we would be super grateful if you filled it in! 🙏
You might have noticed lots of activity in the napari project recently! 🚀 We're grateful for a grant from CZI that's keeping us going, but grants don't last forever: we're trying to figure out sustainable long term funding. Read our blog post to find out how you can help:
napari.org/island-dispa...
napari.org/island-dispa...
November 10, 2025 at 1:23 PM
Remember that survey about how we can sustain napari development? We extended the deadline until the 16th, AoE! Blog post: napari.org/island-dispa...
Survey: napari.typeform.com/sustainability
If you use napari at all we would be super grateful if you filled it in! 🙏
Survey: napari.typeform.com/sustainability
If you use napari at all we would be super grateful if you filled it in! 🙏
Reposted by Michael Doube
We’re switching our eight subscription journals to a #SubscribetoOpen model for 2026. Royal Society Publishing Director, Rod Cookson, explains why and how. royalsociety.org/blog/2025/11... #OpenAccess #S2O
November 10, 2025 at 8:01 PM
We’re switching our eight subscription journals to a #SubscribetoOpen model for 2026. Royal Society Publishing Director, Rod Cookson, explains why and how. royalsociety.org/blog/2025/11... #OpenAccess #S2O
Join me for a tutorial on @bonej.org 17 November 13h00 CET
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...
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...
#HappyFluorescenceFriday #microscopycommunity
Got an idea for an image analysis workshop? Share it at Halfway to I2K: Online Tutorials on Image Analysis (Nov 17–19, 2025), held with Zoom Events!
Submit by Oct 31: buff.ly/lMhK4vz
Website: buff.ly/QP36RZB
Register for the workshops: buff.ly/8nNAI18
Got an idea for an image analysis workshop? Share it at Halfway to I2K: Online Tutorials on Image Analysis (Nov 17–19, 2025), held with Zoom Events!
Submit by Oct 31: buff.ly/lMhK4vz
Website: buff.ly/QP36RZB
Register for the workshops: buff.ly/8nNAI18
November 3, 2025 at 11:00 PM
Join me for a tutorial on @bonej.org 17 November 13h00 CET
Reposted by Michael Doube
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...
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...
#HappyFluorescenceFriday #microscopycommunity
Got an idea for an image analysis workshop? Share it at Halfway to I2K: Online Tutorials on Image Analysis (Nov 17–19, 2025), held with Zoom Events!
Submit by Oct 31: buff.ly/lMhK4vz
Website: buff.ly/QP36RZB
Register for the workshops: buff.ly/8nNAI18
Got an idea for an image analysis workshop? Share it at Halfway to I2K: Online Tutorials on Image Analysis (Nov 17–19, 2025), held with Zoom Events!
Submit by Oct 31: buff.ly/lMhK4vz
Website: buff.ly/QP36RZB
Register for the workshops: buff.ly/8nNAI18
Airtable | Everyone's app platform
Airtable is a low-code platform for building collaborative apps. Customize your workflow, collaborate, and achieve ambitious outcomes. Get started for free.
buff.ly
November 3, 2025 at 10:04 PM
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...
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...
Reposted by Michael Doube
Guess who's back! 🦇
55 years missing: An international team led by the museum rediscovered the Turkestan long-eared bat in the Karakum Desert. Endemic species like 𝘗𝘭𝘦𝘤𝘰𝘵𝘶𝘴 𝘵𝘶𝘳𝘬𝘮𝘦𝘯𝘪𝘤𝘶𝘴 reveal how life adapts – and why protecting unique habitats matters. 🌏
📹 Christian Dietz
#biodiversity #bats
55 years missing: An international team led by the museum rediscovered the Turkestan long-eared bat in the Karakum Desert. Endemic species like 𝘗𝘭𝘦𝘤𝘰𝘵𝘶𝘴 𝘵𝘶𝘳𝘬𝘮𝘦𝘯𝘪𝘤𝘶𝘴 reveal how life adapts – and why protecting unique habitats matters. 🌏
📹 Christian Dietz
#biodiversity #bats
November 3, 2025 at 6:23 PM
Guess who's back! 🦇
55 years missing: An international team led by the museum rediscovered the Turkestan long-eared bat in the Karakum Desert. Endemic species like 𝘗𝘭𝘦𝘤𝘰𝘵𝘶𝘴 𝘵𝘶𝘳𝘬𝘮𝘦𝘯𝘪𝘤𝘶𝘴 reveal how life adapts – and why protecting unique habitats matters. 🌏
📹 Christian Dietz
#biodiversity #bats
55 years missing: An international team led by the museum rediscovered the Turkestan long-eared bat in the Karakum Desert. Endemic species like 𝘗𝘭𝘦𝘤𝘰𝘵𝘶𝘴 𝘵𝘶𝘳𝘬𝘮𝘦𝘯𝘪𝘤𝘶𝘴 reveal how life adapts – and why protecting unique habitats matters. 🌏
📹 Christian Dietz
#biodiversity #bats
Reposted by Michael Doube
Innovative Surfaces to Rapidly Load Bone Implants with Antibiotics
Infectious complications are not uncommon after implant placement. The risk is higher in heavily contaminated wounds, which are particularly common in war zones such as Ukraine, ...
weiterlesen
Infectious complications are not uncommon after implant placement. The risk is higher in heavily contaminated wounds, which are particularly common in war zones such as Ukraine, ...
weiterlesen
November 3, 2025 at 9:41 AM
Innovative Surfaces to Rapidly Load Bone Implants with Antibiotics
Infectious complications are not uncommon after implant placement. The risk is higher in heavily contaminated wounds, which are particularly common in war zones such as Ukraine, ...
weiterlesen
Infectious complications are not uncommon after implant placement. The risk is higher in heavily contaminated wounds, which are particularly common in war zones such as Ukraine, ...
weiterlesen
Wasn't there a job opening at your gaff @jytinevez.bsky.social ...?
Some good news
The Friday crème brûlée is back! @institutpasteur.bsky.social
October 31, 2025 at 9:32 PM
Wasn't there a job opening at your gaff @jytinevez.bsky.social ...?
Gutted to be missing this. Attending in spirit as a head shot staring out at you from this poster!
#GloBIAS2025 is ongoing with amazing speaker lineups at Kobe city
Beautiful location, amazing food and warm bioimage analysis community. What wlse does one need? 😊
Thanks to @globias.bsky.social for this event
Beautiful location, amazing food and warm bioimage analysis community. What wlse does one need? 😊
Thanks to @globias.bsky.social for this event
October 30, 2025 at 11:37 AM
Gutted to be missing this. Attending in spirit as a head shot staring out at you from this poster!