#Cellpose 3 paper now out. Not all images are perfect. Restore your images with Cellpose3 to get better segmentations, w/ @marius10p.bsky.social www.nature.com/articles/s41...
February 12, 2025 at 11:10 AM
#Cellpose 3 paper now out. Not all images are perfect. Restore your images with Cellpose3 to get better segmentations, w/ @marius10p.bsky.social www.nature.com/articles/s41...
Excited to share our paper about copick, a dataset API and toolkit for collaborative annotation and analysis of #cryoET data! Whether you're picking particles or curating segmentations, copick reduces friction and brings #OME-Zarr to cryoET without breaking pipelines.
🧵👇
doi.org/10.1002/pro.70578
🧵👇
doi.org/10.1002/pro.70578
April 20, 2026 at 5:32 PM
Excited to share our paper about copick, a dataset API and toolkit for collaborative annotation and analysis of #cryoET data! Whether you're picking particles or curating segmentations, copick reduces friction and brings #OME-Zarr to cryoET without breaking pipelines.
🧵👇
doi.org/10.1002/pro.70578
🧵👇
doi.org/10.1002/pro.70578
Felix Zhou's u-Segment3D is out:
www.nature.com/articles/s41...
It leverages 2D cell segmentations from orthoviews to generate a ‘consensus’ 3D segmentation.
It does a great job on segmenting densely packed samples, and we have used the algorithm in many applications.
www.nature.com/articles/s41...
It leverages 2D cell segmentations from orthoviews to generate a ‘consensus’ 3D segmentation.
It does a great job on segmenting densely packed samples, and we have used the algorithm in many applications.
November 12, 2025 at 2:41 AM
Felix Zhou's u-Segment3D is out:
www.nature.com/articles/s41...
It leverages 2D cell segmentations from orthoviews to generate a ‘consensus’ 3D segmentation.
It does a great job on segmenting densely packed samples, and we have used the algorithm in many applications.
www.nature.com/articles/s41...
It leverages 2D cell segmentations from orthoviews to generate a ‘consensus’ 3D segmentation.
It does a great job on segmenting densely packed samples, and we have used the algorithm in many applications.
This video was fun. I matched the #Neuroscience segmentations shown first (from the #HHMIJanelia FlyEM team) to the #CellBiology segmentations shown later (from Alyson Petruncio, @herrsaalfeld.bsky.social and the CellMap team). I described the animation with neuVid and rendered it with #Blender.
December 21, 2024 at 9:58 AM
This video was fun. I matched the #Neuroscience segmentations shown first (from the #HHMIJanelia FlyEM team) to the #CellBiology segmentations shown later (from Alyson Petruncio, @herrsaalfeld.bsky.social and the CellMap team). I described the animation with neuVid and rendered it with #Blender.
In #cryoET, separating closely apposed membrane segmentations into distinct labels can be difficult. Small artefacts may connect otherwise separate membranes, requiring tedious slice-by-slice correction. To address this, @jasmred.bsky.social and I developed MemSplit, a napari based workflow.
July 16, 2026 at 8:24 PM
In #cryoET, separating closely apposed membrane segmentations into distinct labels can be difficult. Small artefacts may connect otherwise separate membranes, requiring tedious slice-by-slice correction. To address this, @jasmred.bsky.social and I developed MemSplit, a napari based workflow.
MICrONS explorer allows anyone to explore and download large-scale electron microscopy reconstructions of cortical circuitry from the mouse visual cortex.
🧠📈 Learn how to download images and segmentations in this tutorial from the experts.👇
🧠📈 Learn how to download images and segmentations in this tutorial from the experts.👇
MICrONS Explorer: Downloading Images and Segmentations
alleninstitute.org
February 18, 2025 at 12:51 AM
MICrONS explorer allows anyone to explore and download large-scale electron microscopy reconstructions of cortical circuitry from the mouse visual cortex.
🧠📈 Learn how to download images and segmentations in this tutorial from the experts.👇
🧠📈 Learn how to download images and segmentations in this tutorial from the experts.👇
Our first deposition of synaptic vesicles segmentations is now in the Cryo ET Portal! We segmented vesicles in over 50 tomograms to enable analysis of membrane proteins and more.
cryoetdataportal.czscience.com/depositions/...
cryoetdataportal.czscience.com/depositions/...
February 21, 2025 at 6:57 AM
Our first deposition of synaptic vesicles segmentations is now in the Cryo ET Portal! We segmented vesicles in over 50 tomograms to enable analysis of membrane proteins and more.
cryoetdataportal.czscience.com/depositions/...
cryoetdataportal.czscience.com/depositions/...
April 18, 2025 at 10:44 AM
The weird and wonderful history of British voter segmentations: the names, the ideas, the myths!
From how "the man on the Clapham omnibus" changed English common law to how "Gail's Voter" helped the Lib Dems gain 64 seats in 2024 to what works well when doing segmentation (and what doesn't)
From how "the man on the Clapham omnibus" changed English common law to how "Gail's Voter" helped the Lib Dems gain 64 seats in 2024 to what works well when doing segmentation (and what doesn't)
The Weird and Wonderful History of British Election Voter Segmentations
This "Stockport Man" outlines his ironic (and unironic) love of the a proud British election tradition
jamesbreckwoldt.substack.com
September 9, 2025 at 8:30 AM
The weird and wonderful history of British voter segmentations: the names, the ideas, the myths!
From how "the man on the Clapham omnibus" changed English common law to how "Gail's Voter" helped the Lib Dems gain 64 seats in 2024 to what works well when doing segmentation (and what doesn't)
From how "the man on the Clapham omnibus" changed English common law to how "Gail's Voter" helped the Lib Dems gain 64 seats in 2024 to what works well when doing segmentation (and what doesn't)
Beautiful systematic analysis of membrane thickness inside native cells. This is a great use of both the Chlamy Dataset (bsky.app/profile/cell...) and #MemBrain segmentations (bsky.app/profile/lore...). The open-source workflow is a very helpful resource for #TeamTomo. Thanks and congrats!! 🧪 🔬
Just published! We share an open-source workflow to measure membrane thickness from tomograms, including a tutorial with 3D visualizations. We analyze thickness variations across organelles and reflect on where to define a membrane boundary. @becklab.bsky.social #teamtomo rupress.org/jcb/article/...
November 6, 2025 at 8:51 AM
Beautiful systematic analysis of membrane thickness inside native cells. This is a great use of both the Chlamy Dataset (bsky.app/profile/cell...) and #MemBrain segmentations (bsky.app/profile/lore...). The open-source workflow is a very helpful resource for #TeamTomo. Thanks and congrats!! 🧪 🔬
Baby Open Brains: An open-source dataset of infant brain segmentations | Scientific Data www.nature.com/articles/s41...
Baby Open Brains: An open-source dataset of infant brain segmentations - Scientific Data
Scientific Data - Baby Open Brains: An open-source dataset of infant brain segmentations
www.nature.com
August 19, 2025 at 11:57 PM
Baby Open Brains: An open-source dataset of infant brain segmentations | Scientific Data www.nature.com/articles/s41...
A game changer in our hands... www.nature.com/articles/s41...
Universal consensus 3D segmentation of cells from 2D segmented stacks - Nature Methods
u-Segment3D is a universal framework that translates and enhances 2D instance segmentations to a 3D consensus instance segmentation without training data. It performs well across diverse datasets, inc...
www.nature.com
November 11, 2025 at 6:48 PM
A game changer in our hands... www.nature.com/articles/s41...
Check out @wojwie.bsky.social and @lorenzlamm.bsky.social work on the thylakoid membranes in spinach!
Wojciech stared to long at the segmentations and started seeing Van Goghs in it, so we made his fever dream a reality. More work from #teamthylakoid to come under the starry night skies of Basel!
Wojciech stared to long at the segmentations and started seeing Van Goghs in it, so we made his fever dream a reality. More work from #teamthylakoid to come under the starry night skies of Basel!
November 27, 2024 at 10:28 AM
Check out @wojwie.bsky.social and @lorenzlamm.bsky.social work on the thylakoid membranes in spinach!
Wojciech stared to long at the segmentations and started seeing Van Goghs in it, so we made his fever dream a reality. More work from #teamthylakoid to come under the starry night skies of Basel!
Wojciech stared to long at the segmentations and started seeing Van Goghs in it, so we made his fever dream a reality. More work from #teamthylakoid to come under the starry night skies of Basel!
Roger Benson sent me some amazing CT segmentations of one of the recent fossils found by our team in the Middle Jurassic of Skye & they are incredibly exciting. This is why it is worth being a palaeontologist: the utter joy of the new and unexpected discovery.
February 5, 2026 at 9:05 AM
Roger Benson sent me some amazing CT segmentations of one of the recent fossils found by our team in the Middle Jurassic of Skye & they are incredibly exciting. This is why it is worth being a palaeontologist: the utter joy of the new and unexpected discovery.
This by @jamesbreckwoldt.bsky.social is brilliant: great fun: serious message.
The Weird and Wonderful History of British Election Voter Segmentations
This "Stockport Man" outlines his ironic (and unironic) love of the a proud British election tradition
jamesbreckwoldt.substack.com
September 9, 2025 at 6:41 AM
This by @jamesbreckwoldt.bsky.social is brilliant: great fun: serious message.
Submillimeter Ultra-High Field 9.4 T Brain MR Image Collection and Manual Cortical Segmentations | Scientific Data www.nature.com/articles/s41...
April 24, 2025 at 5:49 AM
Submillimeter Ultra-High Field 9.4 T Brain MR Image Collection and Manual Cortical Segmentations | Scientific Data www.nature.com/articles/s41...
A paired dataset of multi-modal MRI at 3 Tesla and 7 Tesla with manual hippocampal subfield segmentations | Scientific Data www.nature.com/articles/s41...
A paired dataset of multi-modal MRI at 3 Tesla and 7 Tesla with manual hippocampal subfield segmentations - Scientific Data
Scientific Data - A paired dataset of multi-modal MRI at 3 Tesla and 7 Tesla with manual hippocampal subfield segmentations
www.nature.com
February 18, 2025 at 10:39 AM
A paired dataset of multi-modal MRI at 3 Tesla and 7 Tesla with manual hippocampal subfield segmentations | Scientific Data www.nature.com/articles/s41...
this is fair. gender is an example here, but there are many other segmentations.
June 14, 2026 at 11:07 PM
this is fair. gender is an example here, but there are many other segmentations.
Structured Semantic 3D Reconstruction (S23DR-2025) Challenge is live oh HF!
Goal: predict wireframe from SfM point cloud, segmentations and monodepth
Deadline: June 05, 2025
Prize fund: $25 000
#CVPR2025 #USM3D
@cvprconference.bsky.social
huggingface.co/spaces/usm3d...
Library: pip install hoho2025
Goal: predict wireframe from SfM point cloud, segmentations and monodepth
Deadline: June 05, 2025
Prize fund: $25 000
#CVPR2025 #USM3D
@cvprconference.bsky.social
huggingface.co/spaces/usm3d...
Library: pip install hoho2025
April 9, 2025 at 7:57 PM
Structured Semantic 3D Reconstruction (S23DR-2025) Challenge is live oh HF!
Goal: predict wireframe from SfM point cloud, segmentations and monodepth
Deadline: June 05, 2025
Prize fund: $25 000
#CVPR2025 #USM3D
@cvprconference.bsky.social
huggingface.co/spaces/usm3d...
Library: pip install hoho2025
Goal: predict wireframe from SfM point cloud, segmentations and monodepth
Deadline: June 05, 2025
Prize fund: $25 000
#CVPR2025 #USM3D
@cvprconference.bsky.social
huggingface.co/spaces/usm3d...
Library: pip install hoho2025
July 16, 2026 at 11:59 AM
Thanks for the new shorts @jjmalibu.bsky.social 🔥🩳
Taking every chance I get to play with mobility flows and spinal segmentations. Strength is great… but movement longevity is the real goal 👌 #mobilty #sexyshorts #ringmybell
Taking every chance I get to play with mobility flows and spinal segmentations. Strength is great… but movement longevity is the real goal 👌 #mobilty #sexyshorts #ringmybell
March 14, 2026 at 1:54 AM
Thanks for the new shorts @jjmalibu.bsky.social 🔥🩳
Taking every chance I get to play with mobility flows and spinal segmentations. Strength is great… but movement longevity is the real goal 👌 #mobilty #sexyshorts #ringmybell
Taking every chance I get to play with mobility flows and spinal segmentations. Strength is great… but movement longevity is the real goal 👌 #mobilty #sexyshorts #ringmybell
Can't wait to try this out! I have loved seeing my segmentations come to life in Blender
In the context of our @reviewcommons.org revision process, I'm happy to announce Microscopy Nodes v2.2.0!
This packs lots of new fun features, including new color management 🌈, clearer transparency handling 🫥, custom default settings 🔧 and more!
Preprint at doi.org/10.1101/2025...
This packs lots of new fun features, including new color management 🌈, clearer transparency handling 🫥, custom default settings 🔧 and more!
Preprint at doi.org/10.1101/2025...
May 23, 2025 at 11:05 PM
Can't wait to try this out! I have loved seeing my segmentations come to life in Blender
A life lived in #segmentations
Of happiness and sorrow
Inert interstices intertwined —
Dividing up the nectar
Squeezed from the hibiscus
Of a few good days
So that when the gloom
Forces its bitterness
Beyond the sensitive tonsil
The body will not disgorge
All its hope and the need
To survive
#vss365
Of happiness and sorrow
Inert interstices intertwined —
Dividing up the nectar
Squeezed from the hibiscus
Of a few good days
So that when the gloom
Forces its bitterness
Beyond the sensitive tonsil
The body will not disgorge
All its hope and the need
To survive
#vss365
April 18, 2025 at 2:00 PM
A life lived in #segmentations
Of happiness and sorrow
Inert interstices intertwined —
Dividing up the nectar
Squeezed from the hibiscus
Of a few good days
So that when the gloom
Forces its bitterness
Beyond the sensitive tonsil
The body will not disgorge
All its hope and the need
To survive
#vss365
Of happiness and sorrow
Inert interstices intertwined —
Dividing up the nectar
Squeezed from the hibiscus
Of a few good days
So that when the gloom
Forces its bitterness
Beyond the sensitive tonsil
The body will not disgorge
All its hope and the need
To survive
#vss365