Pinned
BoneJ
@bonej.org
· 29d
📢 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.
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.
Reposted by BoneJ
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 BoneJ
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 BoneJ
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
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...
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 10:34 AM
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...
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 10:18 AM
👀
Reposted by BoneJ
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 BoneJ
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.
October 13, 2025 at 4:37 PM
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.
📢 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.
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.
October 13, 2025 at 4:18 PM
📢 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.
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.
Reposted by BoneJ
Do you want to work with Michalis and us on a fun and ambitious LSFM, tracking and gamification project?
Apply!!
Apply!!
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
see www.averof-lab.org/pages/tracman
3/3
October 3, 2025 at 11:16 AM
Do you want to work with Michalis and us on a fun and ambitious LSFM, tracking and gamification project?
Apply!!
Apply!!
🤔
Long, slender trabeculae pass across the marrow space. Trabeculae help resist weightbearing loads. But these ones don't appear to be in a good configuration to do that, unlike the spongy trabeculae nearby.
Maybe they're holding adipose tissue in place, preventing it from wobbling during locomotion?
Maybe they're holding adipose tissue in place, preventing it from wobbling during locomotion?
October 3, 2025 at 10:23 AM
🤔
🤩
The leftovers from last week's bœuf bourguignon. This is a 'marrow bone' after boiling out the adipose tissue for gravy and washing in lots of warm tap water, household detergents and a little chlorine bleach. Cortex & (glorious) trabeculae, growth plate 'scar', marrow cavity visible.
October 3, 2025 at 10:23 AM
🤩
Signed up! Come along and get an intro on BoneJ's features.
Halfway to I2K is BACK, friends of all kinds! Last year, 650 people attended 30+ TOTALLY FREE image analysis workshops of all kinds, across many timezones.
If you make image analysis software and want to teach it, workshop submissions are open now! We'd love to have your tool highlighted.
If you make image analysis software and want to teach it, workshop submissions are open now! We'd love to have your tool highlighted.
#HappyFluorescenceFriday!
#microscopycommunity- want to learn open source image analysis or share your knowledge to help others? We’ve got a FREE virtual workshop Nov 17-19! Now accepting workshop session applications!
Learn more & sign up: buff.ly/esGIotD
#microscopycommunity- want to learn open source image analysis or share your knowledge to help others? We’ve got a FREE virtual workshop Nov 17-19! Now accepting workshop session applications!
Learn more & sign up: buff.ly/esGIotD
October 2, 2025 at 1:03 PM
Signed up! Come along and get an intro on BoneJ's features.
Reposted by BoneJ
📣 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...
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...
📢 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...
cvpd.github.io
September 30, 2025 at 11:01 AM
📣 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...
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...
Reposted by BoneJ
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-...
Bioimage Analysis Specialist | King's College London
www.kcl.ac.uk
September 29, 2025 at 9:48 AM
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-...
🦴 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! 📻
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! 📻
September 25, 2025 at 8:41 AM
🦴 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! 📻
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! 📻
So bad it's good
Rrrr we love the Ccc
Rrrr we love the Ccc
What’s a pirate’s favorite computer programming language?
You’d think it’s R, but no, their first love will always be the C.
Happy talk like a pirate day!
You’d think it’s R, but no, their first love will always be the C.
Happy talk like a pirate day!
a man with a beard is wearing a pirate costume and laughing .
ALT: a man with a beard is wearing a pirate costume and laughing .
media.tenor.com
September 19, 2025 at 9:42 PM
So bad it's good
Rrrr we love the Ccc
Rrrr we love the Ccc
📢 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!
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!
September 16, 2025 at 11:49 AM
📢 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!
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!
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!
September 16, 2025 at 8:28 AM
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!
Reposted by BoneJ
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/paikat/index...
University Researcher in Bioimaging / Universitetsforskare med inriktning bioimaging, 1.11.2025-31.12.2030
abo.rekrytointi.com
September 10, 2025 at 11:28 AM
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/paikat/index...
🔥🔥🔥 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 🤞
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 🤞
September 12, 2025 at 3:43 PM
🔥🔥🔥 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 🤞
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 🤞
Reposted by BoneJ
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...
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...
CBIAS napari workshop 2025
www.crick.ac.uk
September 12, 2025 at 10:08 AM
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...
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...
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!
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!
September 6, 2025 at 12:09 PM
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!
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!
Reposted by BoneJ
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
accessible to scientists and scholars. 👇
#Microscopy @EPFL_en #ImageArchive #DataViz
www.horizons-mag.ch
September 5, 2025 at 6:00 AM
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
accessible to scientists and scholars. 👇
#Microscopy @EPFL_en #ImageArchive #DataViz
📢 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!
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!
September 2, 2025 at 8:24 AM
📢 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!
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!
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.
BoneJ+ will start to work on Intel GPUs and go faster on NVIDIA and AMD too.
😮 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.
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.
August 31, 2025 at 10:22 AM
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.
BoneJ+ will start to work on Intel GPUs and go faster on NVIDIA and AMD too.