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.
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!
Reposted by Michael Doube
Come and join our team 🥰
🚀Join Helsinki BioImaging as an Image Analysis Specialist🖥️to support cross-disciplinary image analysis projects. If you love coding and are interested in working at the crossroads of computer science and biology, apply by 🗓️ November 15, 2025⤵️
jobs.helsinki.fi/job/Helsinki...
#jobopening
jobs.helsinki.fi/job/Helsinki...
#jobopening
Image Analysis Specialist/Engineer/Coordinator, Helsinki Bioimaging
Image Analysis Specialist/Engineer/Coordinator, Helsinki Bioimaging
jobs.helsinki.fi
October 11, 2025 at 8:54 AM
Come and join our team 🥰
Reposted by Michael Doube
#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 2:12 AM
#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
It's totally normal for funders to provide restricted funds that are earmarked for specific activities. It's very unusual to extend restrictions to *all* the recipient's activities, beyond the scope of the funding.
Today it's DEI, tomorrow it could be anything else.
Today it's DEI, tomorrow it could be anything else.
The Python Software Foundation was recommended for a $1.5M grant from the National Science Foundation. The terms of the award said PSF could not work on DEI, whether or not the grant funding was used for it.
PSF therefore declined the funding.
Science suffers, but commitment to core values remains
PSF therefore declined the funding.
Science suffers, but commitment to core values remains
TLDR; The PSF has made the decision to put our community and our shared diversity, equity, and inclusion values ahead of seeking $1.5M in new revenue. Please read and share. pyfound.blogspot.com/2025/10/NSF-...
🧵
🧵
October 28, 2025 at 4:29 PM
It's totally normal for funders to provide restricted funds that are earmarked for specific activities. It's very unusual to extend restrictions to *all* the recipient's activities, beyond the scope of the funding.
Today it's DEI, tomorrow it could be anything else.
Today it's DEI, tomorrow it could be anything else.
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.
DICOM slice position (0020,0032) and not slice thickness (0018,0050) fields are used to determine the size of the image stack.
October 27, 2025 at 11:08 AM
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.
DICOM slice position (0020,0032) and not slice thickness (0018,0050) fields are used to determine the size of the image stack.
Reposted by Michael Doube
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...
Easier said than done: unexpected hurdles to preparing ∼1,000 cranial CT scans for data collection from an online digital repository
Background As science becomes more open and accessible, researchers are increasingly encouraged—and sometimes required—to share their digital data on public repositories. While this promotes transpare...
peerj.com
October 27, 2025 at 7:40 AM
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
DON'T ASSUME THE INSTRUMENT IS PROPERLY CALIBRATED
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.
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...
October 27, 2025 at 10:37 AM
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
DON'T ASSUME THE INSTRUMENT IS PROPERLY CALIBRATED
Reposted by Michael Doube
Heute ist Tag der Bibliotheken
Habt ihr Lieblingsbibliotheken?
Gerne mit Fotos in die Kommentare⬇️
Habt ihr Lieblingsbibliotheken?
Gerne mit Fotos in die Kommentare⬇️
October 24, 2025 at 1:52 PM
Heute ist Tag der Bibliotheken
Habt ihr Lieblingsbibliotheken?
Gerne mit Fotos in die Kommentare⬇️
Habt ihr Lieblingsbibliotheken?
Gerne mit Fotos in die Kommentare⬇️
Reposted by Michael Doube
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...
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
October 23, 2025 at 4:32 PM
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...
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...
Reposted by Michael Doube
#BiologyLetters Sound plays a key role in how animals communicate, but how does hearing develop alongside sound production in fish?https://royalsocietypublishing.org/doi/10.1098/rsbl.2025.0289 #ecology #neuroscience #developmentalbiology
October 22, 2025 at 3:19 PM
#BiologyLetters Sound plays a key role in how animals communicate, but how does hearing develop alongside sound production in fish?https://royalsocietypublishing.org/doi/10.1098/rsbl.2025.0289 #ecology #neuroscience #developmentalbiology