HMS Image Analysis Collaboratory

Day 1 & 2 of #bobiac2025 🐍

With basics of Python in the bag, it was time to analyze images: image handling, pre-processing, cell segmentation and ilastik.

We could not have organized this course without the generous support of @bioimagingna.bsky.social. Thank you!

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!

🎀✨Recording now available ✨🎀

youtu.be/jtDunWK8g1o?...

‼️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/

💻 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...

‼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

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...

Abstract: Three-dimensional subcellular imaging is often hampered by diffraction limits in thick, heterogeneous tissues and invalid assumptions about data distribution and imaging systems. We introduce SSAI-3D, a weakly physics-informed, domain-shift-resistant framework that robustly achieves isotropic 3D imaging. Demonstrations in various label-free samples, plus validation on publicly available 3D datasets with unknown blurring and noise, confirm its potential for more accurate subcellular analysis.

✨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...

💻 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!

Our QuPath course is back!
Join us this semester to learn QuPath with a combination of lectures and hands-on exercises inspired by real research collaborations we worked on.

📌 Introduction to Bioimage Analysis using QuPath
📆 Date: Feb 10, 2025
🔗 tinyurl.com/iac-qupath-2...

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!

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!

Join us next Monday 10 AM EDT for a hybrid Bioimage Analysis Seminar! Jeremy Muhlich (Laboratory of Systems Pharmacology) will talk about image processing and data sharing for whole-slide imaging and spatial profiling of tissues and tumors.

More information: tinyurl.com/3abxjds2

ZIDAS 2024 This one-week school provides a hands-on introduction to image processing and analysis, with an emphasis on biologically relevant examples.

Cross-posting from X.
ZIDAS is coming back home this year to Zurich: A one week, international, bioimage analysis summer school.
8th edition!

Apply here:
2024.zidas.org

We're kicking 2024 with a workshop about the Segment Anything Model (SAM) for Microscopy Data, organized with our friends and neighbors from the Nikon Imaging Center.

Apply here: t.co/yL2sflfqKY