2026-08-14 • 1 post • bsky
Mind boggling, the risks we take. Science is truly no trivial pursuit.
2026-08-04 • 1 post • bsky
debates which torch monitor to use docs.pytorch.org/docs/2.13/mo… or en.wikipedia.org/wiki/Sago_mo…
2026-08-04 • 1 post • bsky
Sometimes it doesn’t matter how many polecats you have
2026-07-24 • 1 post • bsky
Brandeis life science vibes are awesome too!
2026-05-13 • 1 post • bsky
Where do the kitchen towels fit in this
2026-05-13 • 1 post • bsky
A happily ever after about the boids and the bees
2026-04-20 • 1 post • bsky
Also noting that copick is a great example of impactful work that is enabled here at @biohub.org!
2026-04-20 • 1 post • bsky
Woohoo, copick is out! Access to massive amounts of CryoET data, MCP for agentic, plus a @napari.org interface! We even used it when hosting the CZII…
2026-04-10 • 1 post • bsky
Soooo sorry, but “And Betty, when you call me, you can call me Al”
2026-03-18 • 1 post • bsky
This looks awesome! Some gifs would be super cool 😉
2026-03-11 • 1 post • bsky
won’t they just use Daniel Webster?
2026-03-06 • 1 post • bsky
Highly recommended!
2025-12-02 • 1 post • bsky
Great sentiments here, but the semantics aren’t safe quite yet. Models like the ESM family are scientific LLMs that are not chat bots, and the prevale…
2025-10-23 • 1 post • bsky
I love the name!!! Looking forward to checking out🍦
2025-10-12 • 1 post • bsky
Rerun with increased neighbor detection radius
2025-10-09 • 1 post • bsky
This is awesome! Way to go William!!!
2025-10-02 • 1 post • bsky
Howdy #arxiv folks, could someone please endorse my colleague Ambrose Carr on q-bio.QM for a preprint? Endorsement code O488JD thank you!
2025-10-02 • 1 post • bsky
—
2025-09-19 • 1 post • bsky
What about looking at the one person you’re trying to make laugh via DM
2025-08-26 • 1 post • bsky
Caroline Hemphill also wrote up a great blog post about the competition: www.czbiohub.org/life-science…
2025-08-26 • 1 post • bsky
Better ML for cryo-ET starts with better benchmarks. We built a phantom cryo-ET dataset (~500 tomograms) + hosted a Kaggle challenge. The result: co…
2025-08-19 • 1 post • bsky
Is that an anvil?
2025-07-02 • 1 post • bsky
If you post the frames in a thread then we can try scrolling really fast
2025-06-10 • 1 post • bsky
bsky.app/profile/wais…
2025-05-16 • 1 post • bsky
There is a @napari.org hackathon at GloBIAS! Be there or be square (or whatever layer type you’d like)
2025-05-06 • 1 post • bsky
TFW you discover the internet in the conference venue isn’t stable enough for a Google Slides presentation with videos 😅 luckily with >24hr warning
2025-04-26 • 1 post • bsky
We have a suite for studying cell polarity in Python polarityjam.readthedocs.io feel free to post an issue if you need any more functionality
2025-04-07 • 1 post • bsky
“no no, I said turn up the economy”
2025-03-06 • 1 post • bsky
Check this out!!! The results from our CryoET particle picking competition are available, the full test data (public and private datasets) is availabl…
2025-03-05 • 1 post • bsky
Awesome! So glad to see my former RL professor Andy Barto get this recognition (and Rich is too!)
2025-02-12 • 1 post • bsky
Last night we were doing a family dance party… My smartwatch gave a notification… You’ve been running for 5 minutes… I feel judged.
2025-02-05 • 1 post • mastodon
TL;DR installers are really challenging to make. The team made some tooling for @napari that was so fantastic that it is spreading across the scientif…
2025-02-05 • 1 post • bsky
I just want to take the opportunity to remind everyone that the Hamster Dance still exists. You can even find 10 hour long videos of it. YW
2025-02-05 • 1 post • bsky
TL;DR installers are really challenging to make. The team made some tooling for @napari.fosstodon.org.ap.brid.gy that was so fantastic that it is spre…
2025-01-30 • 1 post • bsky
It was the user’s fault for not signing up sooner.
2025-01-30 • 1 post • bsky
🤣
2025-01-30 • 1 post • bsky
is the strategy for getting gemini users to have pop up windows in google apps?
2025-01-23 • 1 post • bsky
AI startup recruiting emails these days: “Our company coming out of stealth mode w new capital. We need a founding engineer for our startup that is fo…
2025-01-21 • 1 post • bsky
For some reason it feels very judgy when my smart watch says “Good job being active again” when I was sitting at my desk scratching my head.
2025-01-16 • 1 post • bsky
I feel your pain. I had to scavenge some emergency J48s a couple of weeks ago.
2025-01-15 • 1 post • bsky
Perfect, you’ve got it! github.com/oanegros/Mic…
2025-01-15 • 1 post • bsky
This is beautiful!!! Do you happen to have some scripts for using Microscopy Nodes w/ bpy in python?
2024-12-29 • 1 post • mastodon
I made some updates to the tiled rendering branch in @napari. If you have uv installed, then this should open the mouse liver FIB-SEM dataset from Ope…
2024-12-29 • 2 posts • bsky
For the @napari.fosstodon.org.ap.brid.gy and large image data out there, I made some updates to the tiled loading zarr demo. It still has limitation…
2024-12-20 • 1 post • bsky
Yes! I’ll write some new code to wrap up the last thing for the year!!!
2024-12-20 • 1 post • bsky
halp
2024-12-18 • 1 post • bsky
First NGFF Mesh call in 42 mins: github.com/ome/ngff/iss…
2024-12-11 • 1 post • bsky
very glad to hear that. @craigreynolds.bsky.social is super cool! we’ve had exchanges about coevolving camouflage over the years, and Craig always kee…
2024-12-09 • 1 post • bsky
The preview of the @chanzuckerberg.bsky.social Virtual Cell Platform just dropped and there is a nice post about behind the scenes of the CZII CryoET
2024-12-08 • 1 post • bsky
For the #ML and #CryoET folks out there: Are folks on here submitting to the CZII CryoET Object Identification competition: www.kaggle.com/competitio…
2024-12-08 • 2 posts • bsky
This work led to awesome camouflage, but I do believe that the power of this approach comes from the coevolutionary/adversairal dynamics. With a visua…
2024-12-04 • 1 post • bsky
Good point, using the micromamba dir in that example is a bit of a red herring. I think using a ~/.envs should be fine.
2024-12-04 • 2 posts • bsky
Conda environments are directories too though… Can you clarify why you’re saying this is a problem for uv? Both make bin, lib subdirs in a target d…
2024-12-04 • 1 post • bsky
uv venv <.venv or .venv2>thensource .venv/bin/activateorsource .venv2/bin/activateIs this enough for you?
2024-11-29 • 1 post • bsky
Posted from @napari.fosstodon.org.ap.brid.gy with #napariBluesky.
2024-11-22 • 1 post • bsky
If folks aren’t aware (especially bioimaging folks), we have a cryoET particle picking competition running (with $$$ prizes): cryoetdataportal.czscie…
2024-11-17 • 1 post • mastodon
https://dev-discuss.pytorch.org/t/pytorch-deprecation-of-conda-nightly-builds/2590 oof, pytorch conda channel is getting deprecated. #python
2024-11-13 • 1 post • mastodon
Are #Python folks I know (especially in the scientific computing area) using rootutils?https://github.com/ashleve/rootutils
2024-11-07 • 1 post • mastodon
Alrighty folks, as promised in https://mastodon.social/@kisharrington/113273799367047306We have launched our cryoET object detection competition! Find…
2024-10-08 • 1 post • mastodon
Huzzah “Open-source Tools for CryoET Particle Picking Machine Learning Competitions” has been accepted at the Machine Learning for Structural Biology
2024-09-14 • 1 post • mastodon
Report: Craig Reynolds’s boids have become more of a nuisance. Now they keep following my hands. Also, they keep leaving a mess behind. As usual, you
2024-09-07 • 1 post • mastodon
Craig Reynolds seems to have let his boids roam free and some are stuck in my house!As usual you can play with the @album solution for this @napari co…
2024-09-06 • 1 post • mastodon
When publishing papers where you need to include your email address I strongly advocate for always using an email address you can always control, I st…
2024-09-05 • 1 post • mastodon
I posted a very early version of an @album codium/vscode extension: https://open-vsx.org/extension/KyleHarrington/album-codeThis ports some of the fun…
2024-08-30 • 1 post • mastodon
My slides for the @napari talk at DL@MBL 2024: https://kephale.github.io/napari-dl-at-mbl-2024/home.htmlIt is just a 1-hr workshop and I’m planning o…
2024-08-30 • 1 post • mastodon
Lol, getting nostalgic while putting the final touches on my presentation at DL @ MBL. I hadn’t really registered that my star detector for finding mi…
2024-08-29 • 1 post • mastodon
It is weird to believe this was 18 years ago, but back in 2006 I presented at my first conference for the 50th Anniversary of Artificial Intelligence
2024-08-22 • 1 post • mastodon
There is always a reason it is discount cheese.
2024-08-17 • 1 post • mastodon
If anyone is in touch with Chris Langton, then please tell him to take his ant back. It is seriously bugging me.Posted as an @album solution for some
2024-08-15 • 1 post • mastodon
Just need a little IZ Kamakawiwoʻole
2024-08-15 • 1 post • mastodon
I’m looking forward to presenting at the 2025 volume EM meeting and the speaker lineup looks awesome!https://www.grc.org/volume-electron-microscopy-co…
2024-08-14 • 1 post • mastodon
These @album slides certainly still need some work, but might as well share them out:https://album-app.github.io/album-tutorial/The cryoET deck:https:…
2024-08-13 • 1 post • mastodon
Me: and they want to copy album installations instead of installing themPartner: so they really want containers5yo: speaking of containers, I need ano…
2024-08-08 • 1 post • mastodon
Langton’s ant is a classic simulation from artificial life. It is super simple: turn right on white, turn left on black, and flip the color the square…
2024-08-05 • 1 post • mastodon
One of the big social shifts I’ve noticed in #Python over the years (even from 2* to 3*) is that everyone seems to be into trains now. Don’t get me wr…
2024-08-04 • 1 post • mastodon
A minimal system of particles with fading tails in @napari. Loosely based on Samuel Yan’s https://openprocessing.org/sketch/1353598Shared as an album
2024-07-27 • 1 post • mastodon
5yo: do you know who is going to be the next president? Me: who? 5yo: Kamala Harris. She’ll be the first girl president.
2024-07-21 • 1 post • mastodon
It is Safety Dance Sunday.
2024-07-19 • 1 post • mastodon
When one plumber says to another “what are you doing are you trying to blow us up"umm… i’m staying on the other side of the house
2024-07-18 • 1 post • mastodon
I had a delightful time on #LastMonkeyStanding with Tom Barbalethttps://www.youtube.com/watch?v=395R__bj-WU
2024-07-17 • 1 post • mastodon
Let’s see how today’s recording for #LastMonkeyStanding goes!
2024-07-16 • 1 post • mastodon
5yo: why do you always say network? Network network network network network networkGotta start early on network and systems sciences
2024-07-08 • 1 post • mastodon
if my grandfather had given me skis, then i probably would have turned them into parentheses.
2024-06-27 • 1 post • mastodon
mmm that fresh desk setup feel
2024-06-25 • 1 post • mastodon
#hottake refrigerator water dispensers should automatically reset to water shortly after you get ice
2024-06-03 • 1 post • mastodon
https://www.biorxiv.org/content/10.1101/2024.05.30.596601v1We made Surforama to support particle picking on surfaces, particularly for cryoET. You can…
2024-05-30 • 1 post • mastodon
it took longer than i care to admit to revisit Talley Lambert’s revised pattern for the Pulser’s library: https://github.com/kephale/pulser/blob/main/…
2024-04-19 • 1 post • mastodon
Just to share a fun upcoming @sciview feature from the ongoing Prague hackathon:Samuel Pantze has added an atmosphere shader so soon you will be able
2024-04-18 • 1 post • mastodon
My muscle memory from C pokes its head out every time I print a bunch of f-strings in python and start writing
printf(...)
2024-04-12 • 1 post • mastodon
When you skip working on multiscale and just go to the highest resolution in your zarr, then take off your mask to reveal that you are Don Diego de la…
2024-03-22 • 1 post • mastodon
Videos in slides should have the following default playback behavior:
2024-03-19 • 1 post • mastodon
a 🔥 minihackathon for album + DL4MicEverywhere across 🇺🇸 🇵🇹 🇩🇪 🇫🇮 #bioimaging #ML will follow up here when the DL4Mic album catalog drops
2024-03-13 • 1 post • mastodon
Some days it feels like it will only be open source (and OSS proximal) folks that will fully embrace OSS. I’m thinking about the cases of choosing an
2024-03-01 • 1 post • mastodon
Who is going to be in Basel next week? #bioimaging
2024-02-23 • 1 post • mastodon
Rocking out to the Pixies like a proper former inhabitant of Western MA
2024-02-08 • 1 post • mastodon
Fonzie bug: a bug that can be resolved by jiggling the UI
2024-02-08 • 1 post • mastodon
Loving @brisvag’s thick slices in @napari. Great way to make your proteins pop
2024-02-06 • 1 post • mastodon
so who is going to be the first to get #emacs working on a vision pro?
2024-02-05 • 1 post • mastodon
I was listening to my music for ~10 minutes before I realized it was at 1.75x speed from watching some lectures earlier….
2024-02-01 • 1 post • mastodon
I have, on occasion, used my fingers to roughly measure how many files I have in one directory compared to another… This is fine.
2024-01-30 • 1 post • mastodon
PolarityJam is out on bioRxiv! Use CellPose, DeepCell, and SAM to segment endothelial cells and analyze their collective dynamics, especially for ques…
2024-01-20 • 1 post • mastodon
TFW you are the only kid in the neighborhood who is outside making a snow fort. Also, you’re over 30.
2024-01-16 • 1 post • mastodon
Inspired by https://twitter.com/hisadan/status/1699354785441571323?s=20.Tooted from #napari with #tootapari.
2024-01-16 • 1 post • mastodon
Playing with an adaptation of the processing code here (https://twitter.com/hisadan/status/1697878658437054785?s=20) to napari.Tooted from #napari wit…
2024-01-16 • 1 post • mastodon
just some yak shaving #emacs, finally trying the switch from #helm -> #vertico, #orderless, #consult, #embark, #marginalia that seems to be sweeping t…
2024-01-11 • 1 post • mastodon
I use bubble sort to organize my part of the house and it shows.
2023-12-31 • 1 post • mastodon
Close all tabs for the new year, orrrrr…
2023-12-23 • 1 post • mastodon
Tis the season for side projects… I started playing with @mikesheldon@octodon.social’s baby_elephant #Mastodon app for #android #watchos. One of my
2023-12-13 • 1 post • mastodon
björk - it’s oh so quiet is a fantastic song for kids
2023-12-08 • 1 post • mastodon
TFW you discover someone you work with on imaging has a similar perspective on how research on biological modeling should proceed. something good is g…
2023-12-04 • 1 post • mastodon
That moment of starting to schedule normal personal ad hoc meetings for the next year…
2023-12-02 • 1 post • mastodon
5yo discovered air quotes
2023-11-30 • 1 post • mastodon
I’m sure there is an aesthetic reason to have light/dark themed template slides use off-white and off-black, but yeesh it is frustrating when using a
2023-11-22 • 1 post • mastodon
What if the real reason for the OpenAI shenanigans was to provide fodder for US Thanksgiving dinner conversations?
2023-11-21 • 1 post • mastodon
The desire to take a week off just so you can focus on a work task for multiple days without needing to context switch.
2023-11-15 • 1 post • mastodon
I’m hiring a Software Engineer to work on ML for CryoET at the new CZ Imaging Institute in Redwood City, CA: https://grnh.se/8394d0275usWe're building…
2023-10-16 • 1 post • mastodon
Get into imaging they said…Explore the dataset they said…
2023-10-16 • 1 post • mastodon
Get into imaging they said…how to get out?
2023-10-11 • 1 post • mastodon
4yo (almost 5) was annoyed about being asked to finish their milk. I found them laying down listening to punk in their room.So proud :D
2023-10-10 • 1 post • mastodon
I livestreamed these blobs here: https://mastodon.social/@couldabeenscience@botsin.space. The #napari hackathon is done and was a success!
2023-09-28 • 1 post • mastodon
Get into imaging they said…
2023-09-26 • 1 post • mastodon
A fun napari script based on this Shadertoy: https://www.shadertoy.com/view/mtyGWyCode here: https://gist.github.com/kephale/ae62ed52f11409e35fcba75b0…
2023-09-22 • 1 post • bsky
Hi all, I’m a computer scientist. Currently I’m focused on computational work that connects to bioimaging data. You can find more about me at my perso…
2023-09-03 • 1 post • mastodon
TFW you play a CD from 25 years ago and you suddenly remember which tracks are scratched
2023-09-02 • 1 post • mastodon
this is a fun video for oat selection.
2023-08-31 • 1 post • mastodon
but who can blame it!
2023-08-27 • 1 post • mastodon
Kitchen sterile technique seems to have gone fine. The blob is growing well enough, but gotta come up with a way to work around the focal plane of the…
2023-08-25 • 1 post • mastodon
Lunch break! Sterile technique, meet kitchen
2023-08-16 • 1 post • mastodon
🏠 🧪 gonna have some fuuuuun this weekend
2023-08-14 • 1 post • mastodon
Fun with Penrose tilings in #napari. Tooted from #napari with #tootapari.
2023-07-21 • 1 post • mastodon
Good times at napari hacking sessions after the CZI Annual Imaging meeting @napari @jni
2023-07-03 • 1 post • mastodon
Just released an update to napari-stable-diffusion! Available: https://www.napari-hub.org/plugins/napari-stable-diffusion. Tooted from #napari with #t…
2023-07-03 • 1 post • mastodon
Another test before releasing 0.0.1 of tootapari. Available here: https://github.com/kephale/tootapari. Tooted from #napari with #tootapari.
2023-07-03 • 1 post • mastodon
Tooted from napari with tootapari.
2023-06-29 • 1 post • mastodon
Tooted from napari with tootapari. still cleaning but this is the first post @napari
2023-06-22 • 1 post • mastodon
In the @napari world, we’ve been working hard on improving volume rendering for large images and there still is more work to do, but please enjoy this…
2023-05-29 • 1 post • mastodon
https://blog.thea.codes/talking-to-gamepads-without-pygame/ is an awesome tutorial by @stargirl
2023-05-15 • 1 post • mastodon
18446744073709551616, you are suspicious too
2023-05-10 • 1 post • mastodon
65536, you suspicious number
2023-03-29 • 1 post • mastodon
Cool, @biovoxxel joined! #imagej #imageanalysis and other folks are probably interested
2023-03-17 • 1 post • mastodon
Cleaning up my notes and… “What if mastodons had funny bones”
2023-03-13 • 1 post • mastodon
#emacs if i wrote an emacs package for archery, then i would call it el.bow. that is all
2023-03-12 • 1 post • mastodon
#emacs #orgmode Does anyone manage their #empv playlist in org-mode? I would appreciate some tips for doing so.I’ve been able to understand the intera…
2023-03-01 • 1 post • mastodon
TFW you’ve been working on a Google Slides deck for a few days, you go back to update a slide and see that someone is visiting another slide. Are surp…
2023-03-01 • 1 post • mastodon
#python 0.0 @ https://www.pola.rs/
2023-02-28 • 1 post • mastodon
#emacs ox-ipynb is great :) that is all.
2023-02-24 • 1 post • mastodon
#emacs in a multi-monitor, macos setup, I often want multiple frames (e.g. separate frames for code+repl and org notes). When using command+tab betwee…
2023-02-17 • 1 post • mastodon
A new version of napari-tyssue is out: https://www.napari-hub.org/plugins/napari-tyssueMostly usability improvements, but one thing of note is that al…
2023-02-17 • 1 post • mastodon
Current browser tab management strategy: semi-randomly decimate open tabs and rely on recently closed tabs in the case of regret.
2023-02-13 • 1 post • mastodon
#bioimaging #microscopy #science #meetings #machinelearning We have an exciting symposium on Machine Learning in Biological Imaging – How to Train You…
2023-02-11 • 1 post • mastodon
#emacs #android how are people setting up your custom init files? like getting emacs to launch with an init read from sd card. im specifically asking
2023-02-09 • 1 post • mastodon
TFW you walk away from a debugging session, have a couple of hours of meetings, and your interpreter is still at your breakpoint and you have to remem…
2023-02-07 • 1 post • mastodon
👋 @perlman
2023-02-07 • 1 post • mastodon
I briefly lost track of this thread, but just in case others need to do command line stuff with #zarr files: https://forum.image.sc/t/cli-programmatic…
2023-02-04 • 1 post • mastodon
Is anyone using #ruff for linting in #emacs?
2023-02-01 • 1 post • mastodon
There is an infinite stream of ChatGPT-driven generative Seinfeld episodes on Twitch https://www.twitch.tv/watchmeforever.
2023-01-30 • 1 post • mastodon
#emacs Has anyone written #orgmode link support for mastodon.el?
2023-01-27 • 1 post • mastodon
After using macos off and on so long with Python dev (noting that I like crashing things), I finally stumbled on https://apple.stackexchange.com/a/250…
2023-01-16 • 1 post • mastodon
#emacs is there a way to work with GitHub projects with magit/forge?
2023-01-16 • 1 post • mastodon
#emacs finally diving into forge, and aside from learning more shortcuts, it was painless. let’s see if it sticks as a workhabit
2022-12-10 • 1 post • mastodon
googling #emacs: how to scratch nose without moving hands from keyboard
2022-11-30 • 1 post • mastodon
HHC day with Breeze and Styles 😊
2022-11-18 • 1 post • mastodon
I moved around the globe from 2019 to 2022, and have concluded that there is no time like home.
2022-11-17 • 1 post • mastodon
Do any #emacs people use #zulip within emacs? e.g. with zulip-helpers.el
2022-11-14 • 1 post • mastodon
I just got my Atreus keyboard (https://shop.keyboard.io/products/keyboardio-atreus). This is my first ergo keyboard in almost forever. These compact l…
2022-11-14 • 1 post • mastodon
what is the best way to do #animatedgifs on mastodon? iirc giphy does a lot of tracking. should we upload the files or is there a #fediverse friendly
2022-11-14 • 1 post • mastodon
It would be cool to get an #artificiallife guppe going @artificiallife
2022-11-09 • 1 post • mastodon
I’ve had some fun with tyssue (https://github.com/DamCB/tyssue). It is a 3D epithelium simulator, and I’m curious if folks other than @glyg on here ar…
2022-11-08 • 1 post • mastodon
With the recent influx, there are some folks I haven’t seen yet. Are the #neuralcellularautomata people on here yet?
2022-11-01 • 1 post • mastodon
What are some fun #profile designs for #mastodon? The metadata table implies some structure…
2022-10-31 • 1 post • mastodon
Hi @billkatz !
2022-10-30 • 1 post • mastodon
For the 3rd year in a row scenery is on the front page of IEEE VIS
2022-10-30 • 1 post • mastodon
my napari stable diffusion plugin is available if anyone wants to test it https://www.napari-hub.org/plugins/napari-stable-diffusion It does run on CP…
2022-10-30 • 1 post • mastodon
#introduction I’m a computer scientist, former professor now software engineer @ CZI. My interests are around image processing, software, and physical…
2022-05-10 • 1 post • mastodon
Deborah Schmidt’s talk on Album is posted https://youtu.be/FUGn3umjuOc