Ultrack on the cover of Nature Methods! Thanks @alexandredizeux.bsky.social for helping us with the beautiful cover art! 😍
Our November issue is now live! 🎉
www.nature.com/nmeth/volume...
On the cover, cell tracking in a developing zebrafish embryo visualized using Ultrack. Cover by Alexandre Dizieux, Jordão Bragantini, Loic Royer, Merlin Lange, CZ Biohub. Paper here: www.nature.com/articles/s41...
www.nature.com/nmeth/volume...
On the cover, cell tracking in a developing zebrafish embryo visualized using Ultrack. Cover by Alexandre Dizieux, Jordão Bragantini, Loic Royer, Merlin Lange, CZ Biohub. Paper here: www.nature.com/articles/s41...
December 1, 2025 at 6:55 PM
Ultrack on the cover of Nature Methods! Thanks @alexandredizeux.bsky.social for helping us with the beautiful cover art! 😍
🧬🔬🧪 🎉 Our team at @czbiohub is thrilled to share TWO companion papers out today in @NatureMethods!
📦 Ultrack — robust, scalable nD cell tracking
🌐 inTRACKtive — a beautiful, open-source web viewer for lineage exploration
Let’s dive in! 👇
www.nature.com/articles/s41...
www.nature.com/articles/s41...
📦 Ultrack — robust, scalable nD cell tracking
🌐 inTRACKtive — a beautiful, open-source web viewer for lineage exploration
Let’s dive in! 👇
www.nature.com/articles/s41...
www.nature.com/articles/s41...
August 25, 2025 at 9:06 AM
🧬🔬🧪 🎉 Our team at @czbiohub is thrilled to share TWO companion papers out today in @NatureMethods!
📦 Ultrack — robust, scalable nD cell tracking
🌐 inTRACKtive — a beautiful, open-source web viewer for lineage exploration
Let’s dive in! 👇
www.nature.com/articles/s41...
www.nature.com/articles/s41...
📦 Ultrack — robust, scalable nD cell tracking
🌐 inTRACKtive — a beautiful, open-source web viewer for lineage exploration
Let’s dive in! 👇
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Second speaker is @teunhuijben.bsky.social from @loicaroyer.bsky.social group at @czbiohub.bsky.social #CBIAS2025
Tracking is hard because segmentation is hard, especially in whole zebra fish embryos: Ultrack can help github.com/royerlab/ult...
Tracking is hard because segmentation is hard, especially in whole zebra fish embryos: Ultrack can help github.com/royerlab/ult...
November 25, 2025 at 11:51 AM
Second speaker is @teunhuijben.bsky.social from @loicaroyer.bsky.social group at @czbiohub.bsky.social #CBIAS2025
Tracking is hard because segmentation is hard, especially in whole zebra fish embryos: Ultrack can help github.com/royerlab/ult...
Tracking is hard because segmentation is hard, especially in whole zebra fish embryos: Ultrack can help github.com/royerlab/ult...
Ultrack is a tool for robust and long-term 3D segmentation in challenging samples such as zebrafish, fruit fly, and nematode embryos.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Ultrack: pushing the limits of cell tracking across biological scales - Nature Methods
Ultrack leverages candidate segmentations from multiple algorithms and temporal consistency across time points for robust, long-term 3D segmentation in challenging samples such as densely packed zebra...
www.nature.com
August 28, 2025 at 8:22 PM
Ultrack is a tool for robust and long-term 3D segmentation in challenging samples such as zebrafish, fruit fly, and nematode embryos.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
I was really happy to play with such data ! this video was created for the Ultrack paper.
#dataviz #scicomm #houdini🧪🔬🐡
#dataviz #scicomm #houdini🧪🔬🐡
August 25, 2025 at 11:58 AM
I was really happy to play with such data ! this video was created for the Ultrack paper.
#dataviz #scicomm #houdini🧪🔬🐡
#dataviz #scicomm #houdini🧪🔬🐡
Our November issue is now live! 🎉
www.nature.com/nmeth/volume...
On the cover, cell tracking in a developing zebrafish embryo visualized using Ultrack. Cover by Alexandre Dizieux, Jordão Bragantini, Loic Royer, Merlin Lange, CZ Biohub. Paper here: www.nature.com/articles/s41...
www.nature.com/nmeth/volume...
On the cover, cell tracking in a developing zebrafish embryo visualized using Ultrack. Cover by Alexandre Dizieux, Jordão Bragantini, Loic Royer, Merlin Lange, CZ Biohub. Paper here: www.nature.com/articles/s41...
November 13, 2025 at 8:38 PM
Our November issue is now live! 🎉
www.nature.com/nmeth/volume...
On the cover, cell tracking in a developing zebrafish embryo visualized using Ultrack. Cover by Alexandre Dizieux, Jordão Bragantini, Loic Royer, Merlin Lange, CZ Biohub. Paper here: www.nature.com/articles/s41...
www.nature.com/nmeth/volume...
On the cover, cell tracking in a developing zebrafish embryo visualized using Ultrack. Cover by Alexandre Dizieux, Jordão Bragantini, Loic Royer, Merlin Lange, CZ Biohub. Paper here: www.nature.com/articles/s41...
Happy to be in sunny☀️San Diego for ASCB Cell Bio! Tomorrow I will present #Ultrack and #inTRACKtive (poster B513) at 11:15 am. Swing by the CZI+@czbiohub.bsky.social
booth (#119) for live demos of these tools + #napari & #zebrahub 🐠 Looking forward to connect!🤩🧪🔬
#CellBio2024 #ASCB24 #celltracking
booth (#119) for live demos of these tools + #napari & #zebrahub 🐠 Looking forward to connect!🤩🧪🔬
#CellBio2024 #ASCB24 #celltracking
December 15, 2024 at 2:33 AM
Happy to be in sunny☀️San Diego for ASCB Cell Bio! Tomorrow I will present #Ultrack and #inTRACKtive (poster B513) at 11:15 am. Swing by the CZI+@czbiohub.bsky.social
booth (#119) for live demos of these tools + #napari & #zebrahub 🐠 Looking forward to connect!🤩🧪🔬
#CellBio2024 #ASCB24 #celltracking
booth (#119) for live demos of these tools + #napari & #zebrahub 🐠 Looking forward to connect!🤩🧪🔬
#CellBio2024 #ASCB24 #celltracking
Kudos @ritastrack.bsky.social for the great years at NMeth!
And congrats to my former colleague Jordao Bragantini for ultrack (and the well deserved cover 🎉) and @teunhuijben.bsky.social for inTRACKtive.
Glad I could contribute to these two wonderful endeavors. GO team @loicaroyer.bsky.social! 🧪🔬
And congrats to my former colleague Jordao Bragantini for ultrack (and the well deserved cover 🎉) and @teunhuijben.bsky.social for inTRACKtive.
Glad I could contribute to these two wonderful endeavors. GO team @loicaroyer.bsky.social! 🧪🔬
I won't talk about NMeth @natmethods.nature.com forever (probably), but I do want to brag a bit about the November focus issue on cell segmentation and tracking, which is many ways is my last hurrah (and final editorial) for the journal. I am so proud of these papers!! www.nature.com/nmeth/volume...
November 13, 2025 at 11:17 PM
Kudos @ritastrack.bsky.social for the great years at NMeth!
And congrats to my former colleague Jordao Bragantini for ultrack (and the well deserved cover 🎉) and @teunhuijben.bsky.social for inTRACKtive.
Glad I could contribute to these two wonderful endeavors. GO team @loicaroyer.bsky.social! 🧪🔬
And congrats to my former colleague Jordao Bragantini for ultrack (and the well deserved cover 🎉) and @teunhuijben.bsky.social for inTRACKtive.
Glad I could contribute to these two wonderful endeavors. GO team @loicaroyer.bsky.social! 🧪🔬
Stunning cover to celebrate the incredible work from @loicaroyer.bsky.social's team.
Learn more about Ultrack, a powerful tool for fast, accurate and scalable cell tracking: biohub.org/life-science... 🧪
Learn more about Ultrack, a powerful tool for fast, accurate and scalable cell tracking: biohub.org/life-science... 🧪
Our November issue is now live! 🎉
www.nature.com/nmeth/volume...
On the cover, cell tracking in a developing zebrafish embryo visualized using Ultrack. Cover by Alexandre Dizieux, Jordão Bragantini, Loic Royer, Merlin Lange, CZ Biohub. Paper here: www.nature.com/articles/s41...
www.nature.com/nmeth/volume...
On the cover, cell tracking in a developing zebrafish embryo visualized using Ultrack. Cover by Alexandre Dizieux, Jordão Bragantini, Loic Royer, Merlin Lange, CZ Biohub. Paper here: www.nature.com/articles/s41...
November 14, 2025 at 7:23 PM
Stunning cover to celebrate the incredible work from @loicaroyer.bsky.social's team.
Learn more about Ultrack, a powerful tool for fast, accurate and scalable cell tracking: biohub.org/life-science... 🧪
Learn more about Ultrack, a powerful tool for fast, accurate and scalable cell tracking: biohub.org/life-science... 🧪
How do you track thousands of cells in complex systems, in 3D & over time? We are launching a Kaggle challenge to push the frontier of AI-powered cell tracking, building on advances like Ultrack & the DaXi lightsheet microscope from the @loicaroyer.bsky.social lab.
bit.ly/4bfdzWE
bit.ly/4bfdzWE
June 29, 2026 at 10:16 PM
How do you track thousands of cells in complex systems, in 3D & over time? We are launching a Kaggle challenge to push the frontier of AI-powered cell tracking, building on advances like Ultrack & the DaXi lightsheet microscope from the @loicaroyer.bsky.social lab.
bit.ly/4bfdzWE
bit.ly/4bfdzWE
Thanks! The cell tracking was done using the software package Ultrack from @jookuma.bsky.social et al, 2025 in @loicaroyer.bsky.social lab!
June 30, 2026 at 8:22 PM
Thanks! The cell tracking was done using the software package Ultrack from @jookuma.bsky.social et al, 2025 in @loicaroyer.bsky.social lab!
Join us next Friday at UC San Diego for a day full of microscopy 💡🔬, mass spec, and AI! Shout out to @manorlaboratory.bsky.social for putting this together! I will present our recent work on cell tracking algorithms and visualization with #Ultrack and #inTRACKtive🧪
#CellBio2024
#CellBio2024
Re-upping this - please register if you're in San Diego this Friday and want to hear about the latest advances in cryoEM/cryoET, mass spec, live imaging, and AI!
tinyurl.com/ASCBSANDBOX
tinyurl.com/ASCBSANDBOX
December 11, 2024 at 4:25 AM
Join us next Friday at UC San Diego for a day full of microscopy 💡🔬, mass spec, and AI! Shout out to @manorlaboratory.bsky.social for putting this together! I will present our recent work on cell tracking algorithms and visualization with #Ultrack and #inTRACKtive🧪
#CellBio2024
#CellBio2024
Happy to be in London for #CBIAS2025! Looking forward to two days of image analysis, and presenting #inTRACKtive and #Ultrack tomorrow 🔬😊
And we’re off. #CBIAS2025 6th Edition, first outside of the Crick but impressed by the localities at @wellcomecollection.bsky.social
@david-j-barry.bsky.social welcoming the community
@david-j-barry.bsky.social welcoming the community
November 24, 2025 at 2:04 PM
Happy to be in London for #CBIAS2025! Looking forward to two days of image analysis, and presenting #inTRACKtive and #Ultrack tomorrow 🔬😊
Amazing work! Happy to see Ultrack used here 😄!
June 30, 2026 at 8:56 PM
Amazing work! Happy to see Ultrack used here 😄!
🔥 In one test (500-frame light-sheet dataset), Ultrack reduced manual corrections by >2× !
Built to work with tools like Cellpose, Stardist, Ilastik.
Open-source, napari-compatible, GPU-accelerated.
awesome data from @adrianjacobo.bsky.social !
Built to work with tools like Cellpose, Stardist, Ilastik.
Open-source, napari-compatible, GPU-accelerated.
awesome data from @adrianjacobo.bsky.social !
August 25, 2025 at 9:06 AM
🔥 In one test (500-frame light-sheet dataset), Ultrack reduced manual corrections by >2× !
Built to work with tools like Cellpose, Stardist, Ilastik.
Open-source, napari-compatible, GPU-accelerated.
awesome data from @adrianjacobo.bsky.social !
Built to work with tools like Cellpose, Stardist, Ilastik.
Open-source, napari-compatible, GPU-accelerated.
awesome data from @adrianjacobo.bsky.social !
4/ 🗺️
This is the problem behind Zebrahub (the Biohub's "Google Earth" of zebrafish development) and Ultrack 📄, our method in Nature Methods 2025 that topped the Cell Tracking Challenge on dense 3D embryos. Now it's your turn to push the state of the art!
This is the problem behind Zebrahub (the Biohub's "Google Earth" of zebrafish development) and Ultrack 📄, our method in Nature Methods 2025 that topped the Cell Tracking Challenge on dense 3D embryos. Now it's your turn to push the state of the art!
June 29, 2026 at 8:00 PM
4/ 🗺️
This is the problem behind Zebrahub (the Biohub's "Google Earth" of zebrafish development) and Ultrack 📄, our method in Nature Methods 2025 that topped the Cell Tracking Challenge on dense 3D embryos. Now it's your turn to push the state of the art!
This is the problem behind Zebrahub (the Biohub's "Google Earth" of zebrafish development) and Ultrack 📄, our method in Nature Methods 2025 that topped the Cell Tracking Challenge on dense 3D embryos. Now it's your turn to push the state of the art!
📄 Ultrack in Nature Methods: www.nature.com/articles/s41...
🌐 inTRACKtive in Nature Methods: www.nature.com/articles/s41...
📦 Code:
github.com/royerlab/ult...
github.com/royerlab/inT...
🧬 Zoo: embryozoo.org
🌐 inTRACKtive in Nature Methods: www.nature.com/articles/s41...
📦 Code:
github.com/royerlab/ult...
github.com/royerlab/inT...
🧬 Zoo: embryozoo.org
www.nature.com
August 25, 2025 at 9:06 AM
📄 Ultrack in Nature Methods: www.nature.com/articles/s41...
🌐 inTRACKtive in Nature Methods: www.nature.com/articles/s41...
📦 Code:
github.com/royerlab/ult...
github.com/royerlab/inT...
🧬 Zoo: embryozoo.org
🌐 inTRACKtive in Nature Methods: www.nature.com/articles/s41...
📦 Code:
github.com/royerlab/ult...
github.com/royerlab/inT...
🧬 Zoo: embryozoo.org
We built these tools because modern light-sheet microscopy generates massive datasets—millions of cells, terabytes of data, hours of embryonic development.
🧠 But data is only half the story. We need to track, explore, and share.
That’s where Ultrack and inTRACKtive come in.
🧠 But data is only half the story. We need to track, explore, and share.
That’s where Ultrack and inTRACKtive come in.
August 25, 2025 at 9:06 AM
We built these tools because modern light-sheet microscopy generates massive datasets—millions of cells, terabytes of data, hours of embryonic development.
🧠 But data is only half the story. We need to track, explore, and share.
That’s where Ultrack and inTRACKtive come in.
🧠 But data is only half the story. We need to track, explore, and share.
That’s where Ultrack and inTRACKtive come in.
💡Ultrack is a robust tracking framework based on multi-hypothesis segmentation & integer linear programming.
It reduces errors dramatically, scales to full embryos, and supports multicolor, 2D/3D, HPC workflows.
More here: github.com/royerlab/ult...
A tour de force by @jookuma.bsky.social
It reduces errors dramatically, scales to full embryos, and supports multicolor, 2D/3D, HPC workflows.
More here: github.com/royerlab/ult...
A tour de force by @jookuma.bsky.social
August 25, 2025 at 9:06 AM
💡Ultrack is a robust tracking framework based on multi-hypothesis segmentation & integer linear programming.
It reduces errors dramatically, scales to full embryos, and supports multicolor, 2D/3D, HPC workflows.
More here: github.com/royerlab/ult...
A tour de force by @jookuma.bsky.social
It reduces errors dramatically, scales to full embryos, and supports multicolor, 2D/3D, HPC workflows.
More here: github.com/royerlab/ult...
A tour de force by @jookuma.bsky.social
It takes Cell-Tracking-Challenge (CTC) output from awesome tracking programs like Trackastra (by @bengallusser.bsky.social) or Ultrack (by @jookuma.bsky.social) & autosaves to CTC output as you go!
Made possible by the great @napari.org ecosystem and tracksdata from @loicaroyer.bsky.social's lab.
Made possible by the great @napari.org ecosystem and tracksdata from @loicaroyer.bsky.social's lab.
September 6, 2026 at 1:09 AM
It takes Cell-Tracking-Challenge (CTC) output from awesome tracking programs like Trackastra (by @bengallusser.bsky.social) or Ultrack (by @jookuma.bsky.social) & autosaves to CTC output as you go!
Made possible by the great @napari.org ecosystem and tracksdata from @loicaroyer.bsky.social's lab.
Made possible by the great @napari.org ecosystem and tracksdata from @loicaroyer.bsky.social's lab.
A new method called Ultrack enables cells to be tracked in 2D & 3D, over time, over different scales & packing densities
📹 @jookuma.bsky.social et al @loicaroyer.bsky.social lab @czbiohub.bsky.social in @natmethods.nature.com
➡️ bpod.org.uk/archive/2025...
📹 @jookuma.bsky.social et al @loicaroyer.bsky.social lab @czbiohub.bsky.social in @natmethods.nature.com
➡️ bpod.org.uk/archive/2025...
September 3, 2025 at 2:28 PM
A new method called Ultrack enables cells to be tracked in 2D & 3D, over time, over different scales & packing densities
📹 @jookuma.bsky.social et al @loicaroyer.bsky.social lab @czbiohub.bsky.social in @natmethods.nature.com
➡️ bpod.org.uk/archive/2025...
📹 @jookuma.bsky.social et al @loicaroyer.bsky.social lab @czbiohub.bsky.social in @natmethods.nature.com
➡️ bpod.org.uk/archive/2025...
Ultrack and inTRACKtive streamline 3D cell tracking and visualization during embryonic development, reducing manual corrections and enabling interactive exploration of diverse whole-embryo datasets.
Ultrack and inTRACKtive: A powerful pair of tools to help track cells through embryonic development
With today's advanced microscopes, scientists can capture videos of entire embryos developing in real time. But there's a catch: turning those breathtaking images into clean, accurate trajectories of each cell's journey as it finds its proper place in a developing organism is incredibly hard.
phys.org
August 25, 2025 at 9:00 AM
Ultrack and inTRACKtive streamline 3D cell tracking and visualization during embryonic development, reducing manual corrections and enabling interactive exploration of diverse whole-embryo datasets.
You might also be interested in motile (github.com/funkelab/mot...) and ultrack (github.com/royerlab/ult...)
GitHub - funkelab/motile: Multi-Object Tracker using Integer Linear Equations
Multi-Object Tracker using Integer Linear Equations - funkelab/motile
github.com
January 24, 2025 at 10:41 AM
You might also be interested in motile (github.com/funkelab/mot...) and ultrack (github.com/royerlab/ult...)
15/ ☎️ If you want to contribute to this project, have a cool dataset that we can feature in the Virtual Embryo Zoo, or need help with cell tracking (with #ultrack), feel free to reach out! More features of #inTRACKtive are on their way, so stay tuned 🤗
November 13, 2024 at 7:53 PM
15/ ☎️ If you want to contribute to this project, have a cool dataset that we can feature in the Virtual Embryo Zoo, or need help with cell tracking (with #ultrack), feel free to reach out! More features of #inTRACKtive are on their way, so stay tuned 🤗