Lightnews — Scholar-powered news

Reposted by Johannes Soltwedel

de.NBI & ELIXIR Germany @denbi.bsky.social · Sep 3

🚀 Registration is open for BioHackathon Germany 2025! Join us 1–5 Dec in Walsrode for hands-on projects, networking, and innovation in #bioinformatics. 🧬🤝
🏨 Anders Hotel Walsrode | 🍽️ Social events | ✈️ Easy travel
🔗 Seats limited—register now! www.denbi.de/de-nbi-event...
#Hackathon

6 9

Johannes Soltwedel @jo-soltwedel.bsky.social · 16d

So it seems like #LinkedIn also wants to start using your personal data to train #AI models 🙄 Opt-out here:

www.linkedin.com/mypreference...

LinkedIn Login, Sign in | LinkedIn

Login to LinkedIn to keep in touch with people you know, share ideas, and build your career.

www.linkedin.com

Reposted by Johannes Soltwedel

Copernicus ECMWF @copernicusecmwf.bsky.social · Aug 20

The new Thermal Trace app from #C3S and #ECMWF is here! 80+ years of thermal stress data based on “feels-like” temperatures for any location worldwide, now at your fingertips. Fast, intuitive, interactive – and free! Read our article for the full details and head to the app. 🔗
bit.ly/46ZMllL

2 26 48

Johannes Soltwedel @jo-soltwedel.bsky.social · Aug 7

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

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

1 8

Reposted by Johannes Soltwedel

BioVoxxel (Jan Brocher) @biovoxxel.de · Jul 21

🎉 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

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

1 4 10

Reposted by Johannes Soltwedel

Brian Northan @truenorth-ia.bsky.social · Jul 21

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-...

GitHub - AlexHego/DL-pixel-classification

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

github.com

2 10 21

Johannes Soltwedel @jo-soltwedel.bsky.social · Jul 21

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

5 1 23

Reposted by Johannes Soltwedel

Virginie Uhlmann @virginieuhlmann.bsky.social · Jul 21

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!!! 🔥🔥🔥

Funded Projects - swissuniversities

www.swissuniversities.ch

2 13 54

Johannes Soltwedel @jo-soltwedel.bsky.social · Jul 18

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!

2 5 25

Johannes Soltwedel @jo-soltwedel.bsky.social · Jul 17

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.

1 4

Reposted by Johannes Soltwedel

EMBRC (European Marine Biological Resource Centre) @embrc-eu.bsky.social · Jul 16

#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/

🌊🧪🦑

6 17

Johannes Soltwedel @jo-soltwedel.bsky.social · Jul 16

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

1

Reposted by Johannes Soltwedel

NumFOCUS @numfocus.bsky.social · Jul 16

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...

10 16

Johannes Soltwedel @jo-soltwedel.bsky.social · Jul 16

#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

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

1 3 15

Reposted by Johannes Soltwedel

Constantin Pape @cppape.bsky.social · Jul 7

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.

1 11 19

Reposted by Johannes Soltwedel

Helmholtz Imaging @helmholtzimaging.helmholtz.social.ap.brid.gy · Jul 2

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]

2 3

Reposted by Johannes Soltwedel

Marcelo Leomil Zoccoler @mazoc.bsky.social · Jul 3

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! ⚙️🔧

Johannes Soltwedel @jo-soltwedel.bsky.social · Jun 17

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...

2 3

Johannes Soltwedel @jo-soltwedel.bsky.social · Jul 3

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

Smoke from wildfires over the city of Dresden

2

Johannes Soltwedel @jo-soltwedel.bsky.social · Jun 17

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!

4

Johannes Soltwedel @jo-soltwedel.bsky.social · Jun 17

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⬆️📈

1 2

Johannes Soltwedel @jo-soltwedel.bsky.social · Jun 17

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!

1 2

Johannes Soltwedel @jo-soltwedel.bsky.social · Jun 17

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:

1 3

Johannes Soltwedel @jo-soltwedel.bsky.social · Jun 17

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...

1 1 5

Johannes Soltwedel @jo-soltwedel.bsky.social · Jun 17

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 👇🧪💻🔬

1 11 29

Reposted by Johannes Soltwedel

Beth Cimini 🔬💻📊 @bethcimini.bsky.social · May 1

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...

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

41 63