Johannes Soltwedel

Download statistics of an open source dataset showing more than 1PB total download volume across all versions. In total, it shows more than 10k and 82k individual downloads

Whenever I feel down, I have a 👀 at the download statistics of that #opensource data-repository I and my team at OncoRay (Dresden) compiled during my PhD at @tudresden.bsky.social @hzdr.bsky.social.

😌

rodare.hzdr.de/record/3131

Basic Microscopic Image Processing and Analysis

Image Analysis Automation with ImageJ Macro Scripting

From Pixels to Patterns: Applied Machine Learning Tools for Advanced Image Analysis

Image Analysis Hero Bundle containing 3 courses 1. Basic Microscopic Image Processing and Analysis 2. Image Analysis Automation with ImageJ Macro Scripting 3. From Pixels to Patterns: Applied Machine Learning Tools for Advanced Image Analysis

🎉 Amazing NEWS for #ImageAnalysis & #LifeSciences folks!
The ultimate #imageanalysis #hattrick is here 🧠🔬✨

www.biovoxxel.de/individual-w...

Read the 🧵👇

All necessary info and links at the end !

#bioimaging #learning #science #lifescience #microscopy #fiji #imagej #machinelearning #deeplearning

GitHub - AlexHego/DL-pixel-classification Contribute to AlexHego/DL-pixel-classification development by creating an account on GitHub.

Great to see @alexhego.bsky.social share instructions on a DL pixel‑classification problem we worked on at image.sc. If you’re working on a challenging 3D DL semantic‑segmentation problem and need more options than most tools provide, check out this repository. github.com/AlexHego/DL-...

Suitable @poldresden.bsky.social farewell cake for a #bioimage analyst? 🥮🤤

Our project BioFAIR: Towards FAIR Practices in Bioimaging has been selected for funding through the swissuniversities Open Science II Programme (www.swissuniversities.ch/en/topics/op...)!

More OME-Zarr and open microscopy community events on the horizon yay!!! 🔥🔥🔥

As good as a time as any to announce: After a great time at @poldresden.bsky.social I'm looking forward to starting my new position at @gerbi-gmb.de as a software developer for @openmicroscopy.org 🔬😀!

Scalable #RDM solutions in the ome-zarr-verse, here we come!

Huh...Voronoi-Otsu, Watershed and Connected Components for the instance segmentation 🤔 The hard part imho is not so much getting a good probability map but rather telling objects apart in dense areas. I could imagine a lot of tuning necessary for each dataset.

#EUProject | #BioImaging & AI

➡️ BioImage Model Zoo by @ai4life.bsky.social is a platform for #AI models in biological imaging

➡️ To find out about the training courses and tools available to help you use the platform correctly for your area of study, visit: www.embrc.eu/project/ai4life/

🌊🧪🦑

Broken gif in original post 😱...better look at the new feature of the @napari.org-clusters-plotter here 👇

Zarr is hiring again! Build scalable bioimaging solutions, collaborate globally, and join the Friedrich Miescher Institute for Biomedical Research as a Computational Scientist or Research Software Engineer
www.fmi.ch/education-ca...

Copying selected elements of a layer in napari into a new layer

#bioimage 🔬 data #visualization and #exploration in @napari.org with the napari-clusters-plotter (0.10.0) becoming yet a bit more versatile: Select objects & put them into new layers for processing, introspection or whatever. Works for all layers, of course! #bioimageanalysis
@mazoc.bsky.social

Are you looking for an exciting position at the intersection of super-resolution microscopy and AI? Then check out the PhD and PostDoc position we offer for a joint project with the Group of Stephan Hell at MPI Göttingen. Please share with anyone interested, read on for links and details.

Reminder: Last chance to join our Helmholtz OMERO workshop!

Learn to organize & annotate your bioimaging data with Fiji, Python & more.

📅 July 17 | Online | 25 seats

Register by July 7 👉 https://events.hifis.net/event/2734/

#HelmholtzImaging #HIFIS […]

[Original post on helmholtz.social]

Check out our latest release of the napari-clusters-plotter plugin! It is so versatile now, try it out with your data! @jo-soltwedel.bsky.social did a great job refactoring a lot of the code to ease its maintainance! ⚙️🔧

Smoke from wildfires over the city of Dresden

@stadt-dresden.bsky.social covered in smoke from earby wildfires. So this really is the new normal, huh...😒 #climatechange

To summarize:
- Unified feature visualization
- Cross layer exploration
- Responsive, extensible design
Try it on your data! And file issues on github.com/BiAPoL/napar... for bugs🐛

Shoutout to @haesleinhuepf.bsky.social @cryaaa.bsky.social @zigutyte for the groundwork on this super-cool project!

Finally some feature processing: I personally find getting a feeling for some #unsupervised #ML parameters hard, e.g., in dimensionality reduction/ #clustering.
Click yourself through the parameters and see what happens interactively!

Needless to say, the algorithms are extensible⬆️📈

Shapes 📐: The new clusters-plotter automatically assigns a fitting colormap to "categorical" features, which is neat when visualizing, e.g. skan (skeleton-analysis.org) #skeletons: Skeleton ids are then automatically assigned fitting colors - no need for manual selections!

With a little help from @stefanhahmann.bsky.social , tracking data is now supported, too. Goes to show the frame-highlighting for #timelapse ⌛data in the new version:

More supported layers: A major upgrade allows to interact with all sorts of @napari.org layer types: Labels🏷️, Points✴️, Vectors🏹, Shapes🔻, Tracks🔀 and even Surfaces⚫!
Particularly cool about Surfaces: @mazoc.bsky.social's histogram view leaves unselected areas transparent!
👉 pypi.org/project/biap...

FINALLY just released the @napari.org clusters-plotter 0.9.0 🤗 pypi.org/project/napa... The latest version comes with a complete overhaul of the entire codebase to make #microscopy data introspection and browsing even more accessible, intuitive and versatile! #bioimaging

Let's have a look 👇🧪💻🔬

Ad for the Bioimage Analysis Beginnings Bootcamp at the Broad Institute. Where & When Broad Institute, 415 Main Street, Cambridge MA (in-person only) Monday–Friday, August 4–8, 20259:00 AM – 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...

Secondly, which I think is very cool: You can now draw annotations in napari and upload them to OMERO. Hopefully this makes annotating large datasets a lot less painful! 💥

(Nevermind my shonky drawing - don't annotate like me 😄)

Looking forward to feedback/bug reports: github.com/tlambert03/n...

New release: napari-omero 0.5.0 😀@openmicroscopy.org @napari.org thanks to some big contributions from @psobolewskiphd.bsky.social , @will-j-moore.bsky.social and of course @talley.codes. Some features in spotlight 👇

First: napari-omero now supports lazy loading of image pyramids from OMERO🔺:

Wait, wait, wait....v0.6.0 is just out, but there is already a next big feature coming to napari? Yes! You see it right 😊 (more impressive demo coming soon) .

Our own @brisvag has been doing work on multichannel grid mode which is to replace our current grid […]

[Original post on fosstodon.org]

That's cool: For a brief amount of time yesterday on May 1st, #solarpower accounted for the entire entire demand of the German grid - and more! Makes me happy to contribute with my measly 800W on my balcony 😅

I quite like this design - I find it easy to compare left and right arch, and the message is about that. Not the absolute quantities over the years.
❤️ 🏳️‍🌈

The Open Microscopy Environment A consortium of universities, research labs, industry and developers producing open-source software and format standards for microscopy data.

Take a gander at those young faces!
www.openmicroscopy.org/teams/ has been updated with the GerBI #OME team's (slightly dated) looks 📸👀
Thrilled to continue contributing to #FAIR data infrastructure @openmicroscopy.org as a part of the @dfg.de funded @nfdi4bioimage.bsky.social and #i3dbio projects!

GitHub - BiAPoL/napari-clusters-plotter at v0.9.0 A napari plugin for clustering objects according to their properties. - GitHub - BiAPoL/napari-clusters-plotter at v0.9.0

We're collecting the work for the next release on a separate branch: github.com/BiAPoL/napar...

Npe2 *and* NAP-06 supported, of course :)

Also, thanks for the compliments 😊

napari-clusters-plotter 0.9.0 is fully npe2 👍