We opened 4 PhD positions at @humantechnopole.bsky.social together with Polimi (see ๐).
My lab offers a PhD project on "Computational Morphogenesis": use state-of-the-art machine learning methods together with realistic simulations to build digital twins of developing tissue.
Apply by March 26.
PAPER OUT โจ How can we make smart microscopy more interoperable? What are the technical and cultural challenges? 30+ people from academia and industry propose a roadmap: doi.org/10.1515/mim-... Also a review of applications and repo of implementations. Join the discussion! smartmicroscopy.github.io
Apply to join #BoBiAC2026 this summer! You'll learn how to use Python to segment fluorescence images w/tools like @ilastik-team.bsky.social & CellposeSAM, & even learn how to measure cell features, neighborhood relationships, & colocalization. No coding experience needed! More info: bobiac.github.io
Apply to join us this July for a crash course on Python & bioimage analysis tailored specifically for beginners! Applications due May 18th ๐ฌ๐ป #BoBiAC2026 bobiac.github.io
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
Organized by @hms-iac.bsky.social & @citehms.bsky.social at Harvard Medical School and sponsored by BioImaging North America @bioimagingna.bsky.social.
๐ฃย We are accepting applications for the 2026 Boston Bioimage Analysis Course (BoBiAC): bobiac.github.io! Join us this July at Harvard Medical School for aย 6-day intensive hands-on courseย to learn bioimage analysis with Python!
Apply by May 18th! No prior Python experience required!
๐งซ->๐ฌ->๐ป->๐
Applications for QI 2026 are due on Friday! ๐ฌ ๐ฅ๏ธ ๐ ๐บ
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.
๐ฌ ๐ฅ๏ธ ๐!
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 Analysisโtwo weeks of advanced imaging, analysis, and hands-on labs with cutting-edge microscopes and open source software!
๐
April 6โ21, 2026
๐ Applications due Friday Jan 30, 2026
๐จ Only a few days left to apply for maybe the best microscopy course there is!!! ๐จ
๐๐๐๐๐๐๐๐๐๐๐
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...
๐ฌ๐จNew preprint alert! ๐จ๐ฌ
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.
๐ฌ ๐ฅ๏ธ Applications are open for the CSHL course Quantitative Imaging: From Acquisition to Analysis (April 6โ21, 2026)!
An intensive, hands-on course covering advanced fluorescence microscopy and quantitative image analysis using open-source tools.
๐๏ธ Apply online by Jan 30, 2026
A fluorescent embryo on black text, with the words Halfway to I2K: Virtual Tutorials on Image Analysis November 17-19, 2025 Virtual Conference for beginners to developers i2kconference.org Image Credit - "Sweet Embryo",Travis D. Carney, BINA Image Contest 2024
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)
Figure legend: Categories and capabilities of smart microscopy systems integrating real-time image analysis and feedback control. Top: Smart microscopy workflows can be classified based on the driving logic behind decision-making: Event-driven (reacting to rare biological events), Outcome-driven (using feedback-control to steer biological systems toward a desired state), Quality-driven (optimizing signal quality or imaging metrics), and Information-driven (guided by models that predict which measurements/perturbations will yield the most informative data). Middle: Central feedback loop between the microscope and an image analysis system, which continuously exchanges images and commands to guide acquisition dynamically. Bottom: Key control actions enabled by smart microscopy: adjusting imaging modality (e.g. switching from brightfield to fluorescence, adjusting sampling rate), repositioning the field of view (e.g. tracking, drift correction), optimizing acquisition settings (e.g. adaptive optics), and performing photomanipulation (e.g. FRAP, ablation, optogenetics).
๐ฌ๐ง 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 ๐
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!
โผ๏ธ3 days left to apply to the Boston Bioimage Analysis Course (BoBiAC)! ๐ป
Get started w/Python & learn to analyze fluorescence microscopy images โ no programming experience required!
Fee waivers available!
๐๏ธ Apply by June 1st!
๐ iac.hms.harvard.edu/bobiac/2025/
custom github css
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
๐ปย Apply to our beginner-friendly Boston Bioimage Analysis Course!
Get started with Python and learn to analyze fluorescence microscopy images โ no coding experience required!
Fee waivers available thanks to funding from @bioimagingna.bsky.social!
๐๏ธ Apply June 1st!
iac.hms.harvard.edu/bobiac/2025/
We are proudly hosting
๐๐ซ. ๐๐๐ฅ๐ฅ๐๐ฒ ๐๐๐ฆ๐๐๐ซ๐ญ @talley.codes (CITE, Harvard Medical School):
๐๐ข๐ฆ๐ฎ๐ฅ๐๐ญ๐ข๐ง๐ ๐ซ๐๐๐ฅ๐ข๐ฌ๐ญ๐ข๐ ๐ฅ๐ข๐ ๐ก๐ญ ๐ฆ๐ข๐๐ซ๐จ๐ฌ๐๐จ๐ฉ๐ฒ ๐ข๐ฆ๐๐ ๐๐ฌ ๐ฎ๐ฌ๐ข๐ง๐ ๐ฆ๐ข๐๐ซ๐จ๐ฌ๐ข๐ฆ
When: ๐๐๐ฒ ๐๐๐ญ๐ก @ ๐๐ ๐๐ฆ ๐๐๐ (Boston time)
Join us on Zoom! harvard.zoom.us/j/9762343464...
Ad for the Bioimage Analysis Beginnings Bootcamp at the Broad Institute. Where & When Broad Institute, 415 Main Street, Cambridge MA (in-person only) MondayโFriday, August 4โ8, 20259:00 AM โ 5:00 PM About the Bootcamp Learn core bioimage analysis skills using open-source tools for light microscopy in this hands-on, in-person course. The Bootcamp covers annotation, segmentation, and deep learning fundamentals. Fee: $600 (Academic/Non-Profit) | $1000 (Industry/For-Profit) For more information email ImagingAdmin@broadinstitute.org
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! ๐ฌ๐ปhttps://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!
โผBREAKINGโผ
Weโve 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
BoBiAC logo incorporating a laptop Boston Bioimage Analysis Course | 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...
