Talley Lambert

My first post here, we have a new preprint out from @aicjanelia.bsky.social! Upright LSFM is fantastic for live imaging, but not amenable to all samples - especially those requiring an air-liquid interface. We worked with Tokai Hit to try to fix that. www.biorxiv.org/content/10.6...

We've spent the last year building something at @humantechnopole.bsky.social that we think is genuinely needed: #AI that works across biological scales and data modalities, not just within them. A thread on what we're doing, why, and who we're looking for. A 🧵... 1/9

Rewrote my Python bioformats wrapper (from aicsimageio/bioio) as a standalone package: - fully bootstrapped Java setup (just pip install) - lazy, repeatably-indexable Array object - fully spec-compliant OME-Zarr group obj. - xarray/dask exports github.com/imaging-form... v0.0.rc1 on PyPI

One of the funniest conversations I've ever had with Claude... stick with it through the third image to watch it slowly realize it's broken, try to "play it cool", fail spectacularly, then attempt self-aware commentary and immediately faceplant again. it's worth it, I promise.

📣 We are accepting applications for the 2026 Boston Bioimage Analysis Course (BoBiAC): bobiac.github.io! Join us this July at Harvard Medical School for a 6-day intensive hands-on course to learn bioimage analysis with Python! Apply by May 18th! No prior Python experience required! 🧫->🔬->💻->📊

QI Class of 2025! Centroid = @sciencedoodles.bsky.social & @florianjug.bsky.social / first minima = @talley.codes & me. Applications for 2026 due on Friday! meetings.cshl.edu/courses.aspx...

🔬 🖥️ Applications are open for the CSHL course Quantitative Imaging: From Acquisition to Analysis (April 6–21, 2026)! An intensive, hands-on course covering advanced fluorescence microscopy and quantitative image analysis using open-source tools. 🗓️ Apply online by Jan 30, 2026

Just played a bit with ty docs.astral.sh/ty/ I’m drooling anticipating the day when the last slow pre-commit hook (mypy/pyright) falls and the entire check is blazing fast ⚡️💨 Maybe not just yet… but so soon

ugh. the macos Tahoe border radius is killing me

it was already fun to look around the documentation for cmap (cmap-docs.readthedocs.io) but @grosoane.bsky.social just added a very cool feature to toggle between color vision deficiencies. Watch your perceptually uniform color maps gain some kinks 😂 as a mild deutan myself, I appreciate it! 🙏

i'm generally thrilled with gh copilot agent recently. There have been multiple very funny cases though where I have asked it to fix a broken test, and the "fix" came in the form of simply deleting the problematic test 😂 "well ... the tests PASS now don't they??"

github.com/hxu296/tariff

Steven has our Snouty-OPM running again after our lab move. He added projection mode, sensorless AO, and a new control GUI based on @talley.codes + crew's pymmcore-plus/pymmcore-gui. Here are some IF-labeled microglia (orange) in the middle of an uncleared 60um mouse brain slice. No deconvolution!

Our openSPIM is officially up and running to image the latest catch of the day! Fueled by pymmcore-plus & pymmcore-gui! 💪⚡🔬 pymmcore-plus.github.io/pymmcore-plus/ github.com/pymmcore-plu...

💻 Announcing the Boston Bioimage Analysis Course — BoBiAC! Join us this July at Harvard Medical School in Boston for a 6-day deep dive into bioimage analysis with Python, hosted by the IAC and CITE. Apply by May 16th, 2025!

www.theguardian.com/technology/2... wish I could say I was surprised...

If you use mkdocs for your python docs, and want quick full API autogen (with navigation) try github.com/tlambert03/m... Particularly if you currently use the mkdocs-gen-files/literatenav/custom-script approach

Join me, @talleylambert.bsky.social, @bethcimini.bsky.social, @florianjug.bsky.social & Hunter Elliott for our two week CSHL course on microscopy & image analysis starting March 24, 2025! Applications are due 1/31/25. meetings.cshl.edu/courses.aspx...

😱📣 BlueSky-ers: WE NEED YOUR HELP!!! 🙏 All of you who ever liked a lecture of mine... All of you who liked one of the courses I teach in... All of you I work(ed) with in one way or another... All of you who see my desperation! 😜 PLEASE re-post! 🙏 careers.humantechnopole.it/o/postdoc-in...

Finally got around to creating a basic Python wrapper for the FPbase API. Hope it helps for those wanting to programmatically retrieve data from FPbase using Python. pip install fpbase github.com/tlambert03/f...

uv now ships with dedicated documentation for PyTorch

If you still default to using `os.path`, this one’s for you:

Hello friends! We’re here to celebrate and share all things fluorescent. Tag us as you share findings related to the use or publication of FPs and other probes

Doing good science is 90% finding a science buddy to constantly talk to about the project.

I feel I specifically should have done better here. (Talky?? Really Talley?)

Six tips for going public with your lab’s software: https://www.nature.com/articles/d41586-024-03344-y 1) make time for maintenance 2) simplify installation 3) add a GUI or good CLI 4) good documentation 5) use github/git 6) automated testing Any other tips people have? #SoftwareEngineering