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

📣 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! 🧫->🔬->💻->📊

Applications for QI 2026 are due on Friday! 🔬 🖥️ 📊 😺

Don't let the price of QI deter you! QI offers financial aid through NCI, HHMS, and @bioimagingna.bsky.social. Include a brief statement of need with your application. Aid is distributed by CSHL (not the course instructors). Many of our students - sometimes all! - receive significant support.

🔬 🖥️ 📊!

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...

Join us at CSHL for Quantitative Imaging: From Acquisition to Analysis—two weeks of advanced imaging, analysis, and hands-on labs with cutting-edge microscopes and open source software! 📅 April 6–21, 2026 📝 Applications due Friday Jan 30, 2026

🚨 Only a few days left to apply for maybe the best microscopy course there is!!! 🚨 👇👇👇👇👇👇👇👇👇👇👇

Re-upping: if you want to learn microscopy and image analysis - REALLY learn them, in an intense and hands on way - this is a really great place to do it. Applications close Jan 30 meetings.cshl.edu/courses.aspx...

🔬🚨New preprint alert! 🚨🔬 We developed quantitative expansion microscopy (qExM) - a method to accurately count proteins in situ by combining expansion microscopy's improved labeling with statistical estimators borrowed from ecology www.biorxiv.org/content/10.6... #SuperResolution #CellBiology

Want to up your microscopy and image analysis game? Applications open now for QI 2026! Join us in cold spring harbor for two weeks of intensive training in all things microscopy.

🔬 🖥️ 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 4 days until the start of I2K and its 33 totally free image analysis tutorials and events! Please share with your "home networks", especially early career researchers - the videos will be amazing and high-impact no matter how many people attend live, BUT (1/x)

🔬🧠 Our paper on smart microscopy & the issue of interoperability! www.biorxiv.org/content/10.1... LONG THREAD WARNING: Smart microscopy uses real-time image analysis to automatically guide the acquisition or perturbation of the sample (closed feedback-control loop). Many applications exist:

Check out our amazing #bobiac2025 cohort! Was a joy to teach this group! Thanks @bioimagingna.bsky.social for generously supporting this 6 week bioimage analysis w/Python course!

Day 1 of #bobiac2025 🐍 The day started strong with @talley.codes speaking about the Python ecosystem and uv. Students then gave short talks about their research (#coolscience). It was then time to code in Python with @sciencedoodles.bsky.social!

‼️3 days left to apply to the Boston Bioimage Analysis Course (BoBiAC)! 💻 Get started w/Python & learn to analyze fluorescence microscopy images — no programming experience required! Fee waivers available! 🗓️ Apply by June 1st! 🌐 iac.hms.harvard.edu/bobiac/2025/

for you other colorblind coders out there, tired of missing the red X in your github actions logs .color-fg-danger, .fgColor-danger {color: magenta !important;} .octicon-x {color: magenta !important;} you're welcome

💻 Apply to our beginner-friendly Boston Bioimage Analysis Course! Get started with Python and learn to analyze fluorescence microscopy images — no coding experience required! Fee waivers available thanks to funding from @bioimagingna.bsky.social! 🗓️ Apply June 1st! iac.hms.harvard.edu/bobiac/2025/

We are proudly hosting 𝐃𝐫. 𝐓𝐚𝐥𝐥𝐞𝐲 𝐋𝐚𝐦𝐛𝐞𝐫𝐭 @talley.codes (CITE, Harvard Medical School): 𝐒𝐢𝐦𝐮𝐥𝐚𝐭𝐢𝐧𝐠 𝐫𝐞𝐚𝐥𝐢𝐬𝐭𝐢𝐜 𝐥𝐢𝐠𝐡𝐭 𝐦𝐢𝐜𝐫𝐨𝐬𝐜𝐨𝐩𝐲 𝐢𝐦𝐚𝐠𝐞𝐬 𝐮𝐬𝐢𝐧𝐠 𝐦𝐢𝐜𝐫𝐨𝐬𝐢𝐦 When: 𝐌𝐚𝐲 𝟐𝟗𝐭𝐡 @ 𝟏𝟏 𝐚𝐦 𝐄𝐃𝐓 (Boston time) Join us on Zoom! harvard.zoom.us/j/9762343464...

BIG NEWS - for the first time ever, we're running a Bioimage Analysis Beginnings Bootcamp. Learn #bioimageanalysis from awesome folks, and gain familiarity with some new tools as well as how to pick the right tool in the first place. Aug 4th-8th - apply here (soon!) forms.gle/d2fCXsrWHVP8...

New to bioimage analysis & Python? Want to quantify fluorescence microscopy images, explore segmentation & classification, & try colocalization analysis using Python? If so, this course is for you! Apply by June 1st! 🔬💻https://iac.hms.harvard.edu/bobiac/2025

Can highly recommend! Not only is Python one of the most versatile tools in bioimage analysis, but bioimage analysis itself is also an excellent way for visual learners to learn and improve their Python skills! And it is led by fantastic people!

‼BREAKING‼ We’ve secured new funding for the Boston Bioimage Analysis Course (BoBiAC) this July at Harvard Med School! Course fees down 37%, with fee waivers for academic applicants, for an intensive hands-on intro to bioimage analysis with Python! Apply by June 1st! iac.hms.harvard.edu/bobiac/2025

Are you looking to boost your bioimage analysis skills? If so, check out the Boston Bioimage Analysis Course run by @hms-iac.bsky.social and @citehms.bsky.social! Apply by 16 May 2025 focalplane.biologists.com/2025/04/10/b...

Please join in-person if you are nearby, or by Zoom if not.

✨We are proudly hosting 𝐏𝐫𝐨𝐟. 𝐒𝐢𝐱𝐢𝐚𝐧 𝐘𝐨𝐮 (MIT)✨ “𝐂𝐨𝐦𝐩𝐮𝐭𝐚𝐭𝐢𝐨𝐧𝐚𝐥 𝐚𝐱𝐢𝐚𝐥 𝐝𝐞𝐛𝐥𝐮𝐫𝐫𝐢𝐧𝐠 𝐟𝐨𝐫 𝐢𝐬𝐨𝐭𝐫𝐨𝐩𝐢𝐜 𝟑𝐃 𝐦𝐢𝐜𝐫𝐨𝐬𝐜𝐨𝐩𝐲” 𝐀𝐩𝐫𝐢𝐥 𝟐𝟒𝐭𝐡 @ 𝟏𝟏 𝐚𝐦 𝐄𝐃𝐓 (𝐁𝐨𝐬𝐭𝐨𝐧 𝐭𝐢𝐦𝐞, 𝐔𝐒𝐀) Join us on Zoom! harvard.zoom.us/j/9307790905...

Great opportunity if you're in the Boston area and want to learn about bioimage analysis in Python! forum.image.sc/t/boston-bio...

Congratulations to students @nancypaniagua.bsky.social & Michal for placing 1st & 2nd place in our @ilastik-team.bsky.social pixel classifier challenge to segment with the least amount of annotations! #lazyannotationsftw

Expansion microscopy of a tardigrade

It's TIRF time again at QI!!! 🎉 🔬Check out @jencwaters.bsky.social's infamous TIRF demo to understand the principle behind total internal reflection vs refraction! #gonetirfing #criticallyawesome

QI 2025 student Federico, a computer scientist, oiling an immersion lens for the first time. 💪

Demonstrating how local environment impacts fluorescence 🔬🧪🥼@qiatcshl.bsky.social

Love this place… 🥰 @qiatcshl.bsky.social @cshlaboratory.bsky.social

I spy with my little eye...a sneak peek of our light sheet microscopy lab samples! Perks of being a @cshlnews.bsky.social course is access to lots of great sample collecting spots! #catchoftheday #tardigrades

Now that looks like a great new course to check out! More python 🐍 heavy than other courses I know… which is great to have! 👍 Check it out, sign up, learn!!! 🤩

This summer, we are running a one-week intensive workshop on Python-based BioImage Analysis. Are there better ways to spend 6 days in mid-July in Boston?Probably. Would you learn as much as you will here? Probably not. Apply here: iac.hms.harvard.edu/bobiac/2025

Excited teach & help w/BoBiAC! This course is perfect for grad students & postdocs using fluorescence microscopy to learn how to use python to process & analyze image data! Best part: it's beginner friendly - no python experience required! More info & apply: iac.hms.harvard.edu/bobiac/2025/...

💻 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!

Team CITE has arrived!

Join us for our first workshops of 2025! 📌 Workshop 1: Image analysis with ImageJ/Fiji 📆 Date: Jan 22 & 24, 2025 🔗 tinyurl.com/iac-fiji-202... 📌 Workshop 2: ImageJ/Fiji's macro language 📆 Date: Jan 28, 2025 🔗 tinyurl.com/iac-fiji-mac... 📍 Location: HMS campus, Boston Open to all—don't miss out!

🔬 Calibrating the DMD for optogenetics. Project light on your cells by drawing in napari-pymmcore!

😱📣 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...

Useful place to start for microscopy and bioimage analysis folks ⬇️⬇️⬇️

@QIatCSHL applications are due Jan 31! 2 weeks of total microscopy & image analysis!! meetings.cshl.edu/courses.aspx...

This microscopy and image analysis course is so good, and so intensive, it should almost be illegal. Apply if you are serious about bio-images!