simonfn.bsky.social - Profile | ThreadSky | a Reddit-style client for Bluesky

Bring your samples into focus! A new version of the #Cellpose cell boundary mapping tool, developed at @hhmijanelia.bsky.social by @computingnature.bsky.social and @marius10p.bsky.social, now works on less-than-perfect microscopy images that are noisy, blurry, or undersampled.

submitted 12 days ago • 0 comments

Thrilled to be teaching this course again this semester! Join us in Boston for an exciting day of learning image analysis, cell detection & classification, spatial analysis and so much more using QuPath. Registration: tinyurl.com/iac-qupath-2...

submitted 44 days ago • 0 comments

I released the LUT finder: A plugin to see all your ImageJ / Fiji LUTs in a table with previews, auto generated descriptions and filtering! You can try it with the KTZ_LUTs update site or from github.com/kwolbachia/L.... I'm looking for your feedbacks! #FluorescenceFriday #MicroscopyMonday

submitted 51 days ago • 2 comments

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!

submitted 52 days ago • 0 comments

Come work with us in the Cimini Lab! The image analysis associate position we're hiring will be working directly with me!

submitted 75 days ago • 0 comments

Best (and most demanding) combined microscopy and image analysis course I know of. Apply!

submitted 89 days ago • 0 comments

Interested in microscopy and/or image analysis? Check out my newest starter pack of super folks.(which also links to the previous, 150-awesome-full one! Both also link to other imaging-y starter packs as I find them) go.bsky.app/MU8c2A2

submitted 107 days ago • 36 comments

Great opportunity to work at the cutting edge of AI applied to biological imaging (and beyond) ⬇️⬇️⬇️

submitted 100 days ago • 0 comments

Feel seen

submitted 103 days ago • 1 comment

We've created a mailing list for Microtutor, our interactive virtual light microscopy courses! Join to learn about new courses: lp.constantcontactpages.com/sl/5BYgJu6/m... Microtutor: microtutor.globalbioimaging.org

submitted 106 days ago • 1 comment

Save the date... our 3rd edition, 2nd hybrid, of this course tailored to bio image analysts. Further info to come soon.

submitted 106 days ago • 0 comments

I made a BioImage Analysts Starter pack. Reachout if you're missing on it 🔬💻🌐 go.bsky.app/2hPEBDu

submitted 112 days ago • 45 comments

I was lucky enough to attend the Workshop where the linked paper was born. You really couldn’t hope to meet a more friendly, clever and approachable bunch, who are all so keen to help other researchers. Check out their Perspective article: journals.biologists.com/jcs/article/... #bioimageanalysis

submitted 110 days ago • 2 comments

I don't think I saw this on social media at all: a bunch of very clever people (including our team) has put together a federated bioimage repository based on OME-Zarr with 500TB of data in 4 months! ome.github.io/ome2024-ngff...

submitted 111 days ago • 3 comments

Like TweetDeck, but better. Because it is here and because it is free.

submitted 113 days ago • 0 comments

Made a starter pack for microscopy and image analysis - please (self-)nominate additions! go.bsky.app/Nwa91pC

submitted 115 days ago • 64 comments

Need a 5-15 minute break from doomscrolling? (You know you do!) Take 5 minutes and tell us how to make #bioimageanalysis #imageanalysis better!

submitted 115 days ago • 2 comments

If you'd like to learn more about the tools available in the Fluorescent Protein Database, FPbase, here's an excellent lecture from creator Talley Lambert! youtu.be/nETkUNQ48Sg

submitted 116 days ago • 1 comment

An excellent primer on co-localization analysis from Federico Gasparoli! youtu.be/Mv4M1HaYdBc @fedegasparoli.bsky.social

submitted 116 days ago • 0 comments

Important commentary on computational analysis in bioimaging Highlights how biology is now a data science (omics, imaging, structure, epidemiology, clinical...) This has major implications for education, training, research culture & infrastructure journals.biologists.com/jcs/article/...

submitted 120 days ago • 0 comments

New from a huge cast of amazing #bioimage analysts in the Journal of Cell Science - "The crucial role of bioimage analysts in scientific research and publication" journals.biologists.com/jcs/article/... . Hop into 🧵to learn more! (1/x) #bioimaging #microscopy #bioimageanalyst

submitted 122 days ago • 1 comment

@carlbergstrom.com The dark side of corvids. They held a multigenerational grudge against my previous dog and would stalk him all over Urbana-Champaign. I thought it was my fanciful imagination until I read this article. www.nytimes.com/2024/10/28/s...

submitted 124 days ago • 0 comments

A classic in dynamical systems: the Lorenz attractor, computed and visualized using #Fiji in #BigDataViewer

submitted 124 days ago • 1 comment

FAIR reuse of FAIR slides at #i2k2024 @ctrue.bsky.social @joshmoore.bsky.social

submitted 127 days ago • 0 comments

If you didn't yet have enough good reasons to share your bioimage data, Matthew, Josh (@joshmoore.bsky.social), Erin, Assaf and I are here with squirrel drawings to convince you that you should do it: journals.biologists.com/jcs/article/...

submitted 127 days ago • 0 comments

PSA from @florianjug.bsky.social to #i2k2024 participants re. lunch---obviously need a script for that

submitted 129 days ago • 0 comments

#i2k2024 let's go! Can't wait!

submitted 129 days ago • 1 comment

With all the new people from twitter, I'm here to say this again: ✨️HITTING THAT REPOST BUTTON IS MORE IMPORTANT THAN LIKES HERE✨️ This site doesn't function like Twitter. It relies on interactions through shares and comments, likes are not as important. Likes do not push posts like the other two do

submitted 134 days ago • 34 comments

Have you ever analyzed a #microscope image before- even just a single one? Please take our survey on progress and places to still improve for image analysis software! #microscopy #imageanalysis #bioimageanalysis forum.image.sc/t/2024-image...

submitted 131 days ago • 1 comment

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

submitted 134 days ago • 0 comments

A tradition - showing off with BigDataViewer. This time by making the ABBA (go.epfl.ch/abba) logo with 4900 multiresolution images, each with a custom affine transform. Smooth when zoomed in, lagging a bit from afar but still very manageable.

submitted 144 days ago • 0 comments

Here's a small recursive image of the Fiji logo made in #ImageJ and #Fiji. Code below.

submitted 144 days ago • 1 comment

Calling all fluorescence microscopy enthusiasts! Whether you're just starting out or you've logged many hours at the microscope, Microtutor LIVE has something new for you. Apply here: tinyurl.com/microtutorli... #microtutor

submitted 194 days ago • 0 comments

If you thought, jeez, I could really use a self-published bench reference for quantitative microscope projects, I have the book for you!

submitted 206 days ago • 1 comment

If ChatGPT and other LLMs are "bullshit-machines", as arguably they are, however crass the term, how shall we think of vision transformers and especially their output in scientific image analysis? HT to Raphael Goncalves for the paper. doi.org/10.1007/s106... en.wikipedia.org/wiki/On_Bull...

submitted 242 days ago • 0 comments

Our first edition of the Northeast Bioimage Analysis Meeting last year was such a success that this year we're having a bigger one; TWO DAYS this time! www.jax.org/education-an...

submitted 281 days ago • 1 comment

Fresh out on biorxiv - me getting to brag about the stupendous, brilliant, AMAZING folks who have been kind enough to come hang out with us at the @broadinstitute to do our Postdoctoral Training Program in #BioimageAnalysis . Into the🧵 for story! www.biorxiv.org/content/10.1... (1/x)

submitted 289 days ago • 2 comments

From Images to Knowledge (I2K) is going down at Human Technopole in Milan, Italy, from October 23-25 2024. 🗓️ 🚨 Abstract and Workshop submission now OPEN 🚨https://forms.gle/E2McVjKU1sAsF97Q9 Invited speakers will soon be announced, but most talks will be selected from your🫵 abstracts!!!

submitted 330 days ago • 1 comment

Honed by many rounds of collaborative paper writing with PhD students and postdocs, my list of 24 scientific writing tips: www.huber.embl.de/group/posts/... Subjective and personal, but hopefully useful for somebody.

submitted 341 days ago • 2 comments

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

submitted 360 days ago • 0 comments

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

submitted 381 days ago • 0 comments

Opening: Permanent position for bioimage analyst in Uppsala, Sweden. Group of lovely people there. forum.image.sc/t/bioinforma...

submitted 393 days ago • 0 comments

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

submitted 399 days ago • 0 comments