Nathan Clack
@nclack.bsky.social
Reposted by Nathan Clack
If you'd like any programming practice, I have ten years (soon: 11) of programming puzzles on adventofcode.com!
All of the puzzles are completely free! This is possible in part due to some lovely sponsors who you should definitely check out: adventofcode.com/2025/sponsors
All of the puzzles are completely free! This is possible in part due to some lovely sponsors who you should definitely check out: adventofcode.com/2025/sponsors
November 28, 2025 at 2:48 PM
If you'd like any programming practice, I have ten years (soon: 11) of programming puzzles on adventofcode.com!
All of the puzzles are completely free! This is possible in part due to some lovely sponsors who you should definitely check out: adventofcode.com/2025/sponsors
All of the puzzles are completely free! This is possible in part due to some lovely sponsors who you should definitely check out: adventofcode.com/2025/sponsors
Reposted by Nathan Clack
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...
October 21, 2025 at 2:32 PM
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...
Reposted by Nathan Clack
🧠 The Lipid #Brain Atlas is out now! If you think #lipids are boring and membranes are all the same, prepare to be surprised. Led by @lucafusarbassini.bsky.social with Giovanni D'Angelo's lab, we mapped membrane lipids in the mouse brain at high resolution.
www.biorxiv.org/cgi/content/...
www.biorxiv.org/cgi/content/...
October 16, 2025 at 6:23 AM
🧠 The Lipid #Brain Atlas is out now! If you think #lipids are boring and membranes are all the same, prepare to be surprised. Led by @lucafusarbassini.bsky.social with Giovanni D'Angelo's lab, we mapped membrane lipids in the mouse brain at high resolution.
www.biorxiv.org/cgi/content/...
www.biorxiv.org/cgi/content/...
Reposted by Nathan Clack
Join us as we explore emerging trends in agentic AI applications across bioinformatics workflows.
✨ Featured Panelists:
Kexin Huang - Stanford University
Vega Shah, PhD - NVIDIA
Loic Royer - Chan Zuckerberg Biohub Network
Jonah Cool - Anthropic
✨ Featured Panelists:
Kexin Huang - Stanford University
Vega Shah, PhD - NVIDIA
Loic Royer - Chan Zuckerberg Biohub Network
Jonah Cool - Anthropic
October 3, 2025 at 3:43 PM
Join us as we explore emerging trends in agentic AI applications across bioinformatics workflows.
✨ Featured Panelists:
Kexin Huang - Stanford University
Vega Shah, PhD - NVIDIA
Loic Royer - Chan Zuckerberg Biohub Network
Jonah Cool - Anthropic
✨ Featured Panelists:
Kexin Huang - Stanford University
Vega Shah, PhD - NVIDIA
Loic Royer - Chan Zuckerberg Biohub Network
Jonah Cool - Anthropic
Reposted by Nathan Clack
I gave a talk at Blender Conference yesterday, showing how biological volumes work, and how to visualize them in Blender 😋 youtu.be/WPajSWX730o?... #bcon25
Microscopy Nodes: handling large biological volumes — Blender Conference 2025
YouTube video by Blender
youtu.be
September 19, 2025 at 7:35 AM
I gave a talk at Blender Conference yesterday, showing how biological volumes work, and how to visualize them in Blender 😋 youtu.be/WPajSWX730o?... #bcon25
Reposted by Nathan Clack
Tomorrow is #VivaCalleSJ! Roughly 10 miles of streets across San Jose will be closed to cars. Organizers estimate ~150,000 participants.
Here’s the map, and vivacallesj.org has details on events across the network. 10am to 3pm Sunday.
LFG!
#dtsj #openstreets
Here’s the map, and vivacallesj.org has details on events across the network. 10am to 3pm Sunday.
LFG!
#dtsj #openstreets
September 6, 2025 at 8:41 PM
Tomorrow is #VivaCalleSJ! Roughly 10 miles of streets across San Jose will be closed to cars. Organizers estimate ~150,000 participants.
Here’s the map, and vivacallesj.org has details on events across the network. 10am to 3pm Sunday.
LFG!
#dtsj #openstreets
Here’s the map, and vivacallesj.org has details on events across the network. 10am to 3pm Sunday.
LFG!
#dtsj #openstreets
Reposted by Nathan Clack
🧬🔬🧪 🎉 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...
Reposted by Nathan Clack
🚀 Big news! The napari hub has been reimplemented and is now community-run! :tada: It's still the go-to place for finding and sharing napari plugins, but the website is now snappier and lighter-weight. Check it out 👉 www.napari-hub.org
July 23, 2025 at 5:24 PM
🚀 Big news! The napari hub has been reimplemented and is now community-run! :tada: It's still the go-to place for finding and sharing napari plugins, but the website is now snappier and lighter-weight. Check it out 👉 www.napari-hub.org
Reposted by Nathan Clack
🥰 Self-supervised, label-free 3D cell imaging is here
Congrats to Cyril on this very cool first, first author publication 🏆! This started when he was a bachelor's student (and he's now completing his masters!).
And many thanks to my other awesome co-authors🙏
elifesciences.org/articles/99848
Congrats to Cyril on this very cool first, first author publication 🏆! This started when he was a bachelor's student (and he's now completing his masters!).
And many thanks to my other awesome co-authors🙏
elifesciences.org/articles/99848
Self-supervised, label-free 3D cell imaging is here
EPFL researchers introduce CellSeg3D, a self-supervised tool for 3D cell segmentation in fluorescence microscopy, eliminating the need for manual labeling and enhancing accessibility for various biolo...
actu.epfl.ch
June 24, 2025 at 5:53 PM
🥰 Self-supervised, label-free 3D cell imaging is here
Congrats to Cyril on this very cool first, first author publication 🏆! This started when he was a bachelor's student (and he's now completing his masters!).
And many thanks to my other awesome co-authors🙏
elifesciences.org/articles/99848
Congrats to Cyril on this very cool first, first author publication 🏆! This started when he was a bachelor's student (and he's now completing his masters!).
And many thanks to my other awesome co-authors🙏
elifesciences.org/articles/99848
Reposted by Nathan Clack
Hello Fly Folks. quick note FlyBase is under duress due to termination NIH$ to Harvard and intl collabs. The hardworking folks @flybase.bsky.social are doing their darndest to ensure access to current data. For US, there will soon be a new site to donate. Please spread the word, ideas and support 🪰💪
My lab studies bacterial infections. We spend a lot of time looking at (or for) species-specific genetic and genomic databases for hosts and microbes. FlyBase is the best of all—there is literally no comparison. Its existence is under threat. Please donate.
www.philanthropy.cam.ac.uk/give-to-camb...
www.philanthropy.cam.ac.uk/give-to-camb...
Drosophila Genetic Database
The Drosophila Genetic Database, FlyBase, is on the brink of collapse due to the sudden termination of the FlyBase NIH grant, which includes salaries for 5 literature curators based at the University ...
www.philanthropy.cam.ac.uk
June 4, 2025 at 3:07 PM
Hello Fly Folks. quick note FlyBase is under duress due to termination NIH$ to Harvard and intl collabs. The hardworking folks @flybase.bsky.social are doing their darndest to ensure access to current data. For US, there will soon be a new site to donate. Please spread the word, ideas and support 🪰💪
Reposted by Nathan Clack
🧠 Janelia researchers have developed a new way to map how individual connections between neurons change across the entire brain during learning, giving scientists a new view into how changes in behavior show up in the brain. www.janelia.org/news/new-ima...
May 26, 2025 at 3:56 PM
🧠 Janelia researchers have developed a new way to map how individual connections between neurons change across the entire brain during learning, giving scientists a new view into how changes in behavior show up in the brain. www.janelia.org/news/new-ima...
Reposted by Nathan Clack
Wanted to share some key takeaways from this meeting for the broader public. If you were there and I missed things, please add on to this thread!
I am in sunny San Francisco for a meeting on AI in bioimaging at CZI headquarters! Looking forward to 🤯🤩 data and great conversations!
May 15, 2025 at 4:39 PM
Wanted to share some key takeaways from this meeting for the broader public. If you were there and I missed things, please add on to this thread!
Reposted by Nathan Clack
Any scikit-image fans in Vienna? The skimage team would like to meet in Vienna for a code sprint Aug 14-16 ahead of EuroSciPy. We'd super appreciate it if someone's workplace can host us! All we need is electricity, natural light, and (most important) walking distance to coffee. ☕️😂🙏
May 15, 2025 at 7:19 AM
Any scikit-image fans in Vienna? The skimage team would like to meet in Vienna for a code sprint Aug 14-16 ahead of EuroSciPy. We'd super appreciate it if someone's workplace can host us! All we need is electricity, natural light, and (most important) walking distance to coffee. ☕️😂🙏
Reposted by Nathan Clack
🚀🔬🦠 Releasing 🤖Cellpose-SAM🤖, a cellular segmentation algorithm with superhuman generalization 🦸♀️. Try it now on 🤗 huggingface.co/spaces/mouse...
paper: www.biorxiv.org/content/10.1...
w/ @computingnature.bsky.social 1/n
paper: www.biorxiv.org/content/10.1...
w/ @computingnature.bsky.social 1/n
May 3, 2025 at 7:12 PM
🚀🔬🦠 Releasing 🤖Cellpose-SAM🤖, a cellular segmentation algorithm with superhuman generalization 🦸♀️. Try it now on 🤗 huggingface.co/spaces/mouse...
paper: www.biorxiv.org/content/10.1...
w/ @computingnature.bsky.social 1/n
paper: www.biorxiv.org/content/10.1...
w/ @computingnature.bsky.social 1/n
Reposted by Nathan Clack
Thanks to @liu-hanjin.bsky.social, napari now has a command palette! 🎨 This thing is really nice to use — the core team can no longer live without it — and it even works with plugin commands! 🤩
April 11, 2025 at 10:27 AM
Thanks to @liu-hanjin.bsky.social, napari now has a command palette! 🎨 This thing is really nice to use — the core team can no longer live without it — and it even works with plugin commands! 🤩
Reposted by Nathan Clack
How can AI help you to analyze your microscopy images?
Find out at the "Machine Learning for Microscopy Image Analysis" course at the @mblscience.bsky.social in Woods Hole from Aug 22-Sep 6!
Applications are due 🚨 April 30 🚨
Read on for more! 👇
www.mbl.edu/education/ad...
Find out at the "Machine Learning for Microscopy Image Analysis" course at the @mblscience.bsky.social in Woods Hole from Aug 22-Sep 6!
Applications are due 🚨 April 30 🚨
Read on for more! 👇
www.mbl.edu/education/ad...
AI@MBL: Machine Learning for Microscopy Image Analysis | Marine Biological Laboratory
The goal of this course is to familiarize researchers in the life sciences with state-of-the-art deep learning techniques for microscopy image analysis and to introduce them to tools and frameworks th...
www.mbl.edu
April 18, 2025 at 6:48 PM
How can AI help you to analyze your microscopy images?
Find out at the "Machine Learning for Microscopy Image Analysis" course at the @mblscience.bsky.social in Woods Hole from Aug 22-Sep 6!
Applications are due 🚨 April 30 🚨
Read on for more! 👇
www.mbl.edu/education/ad...
Find out at the "Machine Learning for Microscopy Image Analysis" course at the @mblscience.bsky.social in Woods Hole from Aug 22-Sep 6!
Applications are due 🚨 April 30 🚨
Read on for more! 👇
www.mbl.edu/education/ad...
Reposted by Nathan Clack
🧬🔬🧪 We are seeking a Scientist to push the limits of spatial transcriptomics in zebrafish! Come join us!
#MolBio #SpatialTranscriptomics #DevelopmentalBiology #ScienceJobs 🧫🐟🔍
job-boards.greenhouse.io/chanzuckerbe...
#MolBio #SpatialTranscriptomics #DevelopmentalBiology #ScienceJobs 🧫🐟🔍
job-boards.greenhouse.io/chanzuckerbe...
Scientist, Spatial Molecular Cartography (Jacobo/Royer Group - Biohub SF)
San Francisco, California, United States
job-boards.greenhouse.io
April 15, 2025 at 6:27 PM
🧬🔬🧪 We are seeking a Scientist to push the limits of spatial transcriptomics in zebrafish! Come join us!
#MolBio #SpatialTranscriptomics #DevelopmentalBiology #ScienceJobs 🧫🐟🔍
job-boards.greenhouse.io/chanzuckerbe...
#MolBio #SpatialTranscriptomics #DevelopmentalBiology #ScienceJobs 🧫🐟🔍
job-boards.greenhouse.io/chanzuckerbe...
Reposted by Nathan Clack
2025 = 45^2
It's a perfect square. It will probably be the only perfect square year you ever get to live in.
The last time that occurred was in 1936. The next will be in 2116.
So, make 2025 a perfect year for you.
It's a perfect square. It will probably be the only perfect square year you ever get to live in.
The last time that occurred was in 1936. The next will be in 2116.
So, make 2025 a perfect year for you.
December 31, 2024 at 3:32 PM
2025 = 45^2
It's a perfect square. It will probably be the only perfect square year you ever get to live in.
The last time that occurred was in 1936. The next will be in 2116.
So, make 2025 a perfect year for you.
It's a perfect square. It will probably be the only perfect square year you ever get to live in.
The last time that occurred was in 1936. The next will be in 2116.
So, make 2025 a perfect year for you.
Reposted by Nathan Clack
⚡️ Excited to introduce ZAPBench, our #ICLR2025 spotlight: The Zebrafish Activity Prediction Benchmark measures progress in predicting neural activity within an entire vertebrate brain (70k+ neurons!)
Explore interactive visualizations, datasets, code + paper: google-research.github.io/zapbench
🧠🧪
Explore interactive visualizations, datasets, code + paper: google-research.github.io/zapbench
🧠🧪
ZAPBench
ZAPBench evaluates how well different models can predict the activity of over 70,000 neurons in a novel larval zebrafish dataset.
google-research.github.io
March 4, 2025 at 3:22 PM
⚡️ Excited to introduce ZAPBench, our #ICLR2025 spotlight: The Zebrafish Activity Prediction Benchmark measures progress in predicting neural activity within an entire vertebrate brain (70k+ neurons!)
Explore interactive visualizations, datasets, code + paper: google-research.github.io/zapbench
🧠🧪
Explore interactive visualizations, datasets, code + paper: google-research.github.io/zapbench
🧠🧪
Reposted by Nathan Clack
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/...
Reposted by Nathan Clack
Holy shit, nerds, have you seen this? If you're studying #brain wide neuronal activation using #cFOS and a #lightsheet #microscope you need to read this doc STAT🧪🔬.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
A deep learning pipeline for three-dimensional brain-wide mapping of local neuronal ensembles in teravoxel light-sheet microscopy - Nature Methods
The ACE pipeline utilized deep learning and advanced statistics for mapping neural activity at a granular level that is independent of atlas-defined regions.
www.nature.com
January 30, 2025 at 12:52 AM
Holy shit, nerds, have you seen this? If you're studying #brain wide neuronal activation using #cFOS and a #lightsheet #microscope you need to read this doc STAT🧪🔬.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Nathan Clack
And now, support for Zarr v3 & sharding is released as an OME-Zarr specification! 🎉
forum.image.sc/t/ngff-0-5-r...
#NGFF #BioImaging #Formats
@openmicroscopy.org @zarr.dev
forum.image.sc/t/ngff-0-5-r...
#NGFF #BioImaging #Formats
@openmicroscopy.org @zarr.dev
January 28, 2025 at 3:42 PM
And now, support for Zarr v3 & sharding is released as an OME-Zarr specification! 🎉
forum.image.sc/t/ngff-0-5-r...
#NGFF #BioImaging #Formats
@openmicroscopy.org @zarr.dev
forum.image.sc/t/ngff-0-5-r...
#NGFF #BioImaging #Formats
@openmicroscopy.org @zarr.dev
Reposted by Nathan Clack
This was my tenth(!) year building 25 days of puzzles for #AdventOfCode. You can solve them all for free! Most people write code to solve them, but you can solve them however you like. I hope they help people become better programmers. 🌟
The first puzzle comes out in two hours: adventofcode.com
The first puzzle comes out in two hours: adventofcode.com
Advent of Code 2024
adventofcode.com
December 1, 2024 at 2:57 AM
This was my tenth(!) year building 25 days of puzzles for #AdventOfCode. You can solve them all for free! Most people write code to solve them, but you can solve them however you like. I hope they help people become better programmers. 🌟
The first puzzle comes out in two hours: adventofcode.com
The first puzzle comes out in two hours: adventofcode.com