Day 4 open software week #OSW by @neuroinformatics.dev, Hackday!

It was really a cool experience to see people from different backgrounds coming together and try things, learn with each other and contributing to open source resources

Thanks a lot to the instructors for guiding and supporting us!

Day 4 of the open software week #OSW, all about big jmaging data and @zarr.dev @openmicroscopy.org

One of my favorite days so far, lots of discussions with mang experts in the field from very different backgrounds. I understood Zarr much better and we got to write blog posts on selected topics!

Day 1 of Open Software Week #OSW organized by @neuroinformatics.dev!

Really impressed with everything I've seen so far. Great lecture material, great team synergies and great organization.

Wanna peak at the material? Take a look here: neuroinformatics.dev/open-softwar...

Looking forward to Day 2!

I'm headed to London where in the next two weeks I'll learn from the amazing people at @neuroinformatics.dev!

I'm super excited for the open software week #OSW to learn all about large image data handling, @brainglobe.info and much more!

And here's the full labeling by one of our users for the full training patch. Some errors to still correct, but such a time saver!

We've been trying nnInteractive (github.com/MIC-DKFZ/nap...) to quickly create labeled data for later training an Omnipose model. I whatever black magic you did there, keep at it! It's such a life-changer!

We also invited @haesleinhuepf.bsky.social who gave us an excellent and super relevant talk about "Learning and Training #BioImageAnalysis in the Age of AI".

His experience in image analysis and teaching gave further push to the initiative with concrete solutions. Thank you for joining!

During the event, we had the honor of having the Director of Curriculum @tobyhodges.bsky.social himself giving us an intro to @carpentries.carpentries.org philosophy and goals.

He provided essential wisdom and guidance in steering the discussion for the course approach and content. Thank you, Toby!

In the past 2 days, we had the great pleasure to host an in-person workshop at @istaresearch.bsky.social with the collaboration of @globias.bsky.social, @carpentries.carpentries.org and @istaustria-iof.bsky.social.

We wanted to create a go-to course for image analysis in Python. Info in the thread!

As part of our regular health check of our systems at @istaustria-iof.bsky.social, we acquire and analyze flat-field images automatically through our internal database.

Today I noticed a particularly strange FF image my script analyzed, but of course I am going to leave it there! 😂

Let's give it a go to my first #FluorescenceFriday
Here's a color-coded Z-projection of a weevil head imaged on our Zeiss light-sheet 7 with pure green autofluorescence.

Looking very cool, but also ominous!

@istaustria-iof.bsky.social

Don't you hate it when the last time you modified your Jupyter notebook was *next year*? 😂

I think I'm getting addicted to new #BigTrace in #Fiji by @ekatrukha.bsky.social 😅 So satisfying!
Here's a live demo as I segment an entire notochord using the 'one-click' tracking tool and instantly straighten the entire thing for later analysis!
Try it out here: github.com/ekatrukha/Bi...