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Big Thanks to Robert Haase for making #PoLBIAS23 happen.

Mastodon Deep Lineage 0.0.1 released and uploaded to Fiji update site. Release Notes: github.com/mastodon-sc/ma… Update Site: sites.imagej.net/Mastodon-DeepL… Demonstration of functions: youtube.com/watch?v=774VE5…

A presentation about classification of lineage trees in Mastodon uploaded to Zenodo: doi.org/10.5281/zenodo…

Out last week from the Tinevez and Olivo-Marin labs! JDLL: a library to run deep learning models on Java bioimage informatics platforms. This is sure to streamline deployment of DL models in bioimaging. nature.com/articles/s4159…

Mastodon Deep Lineage 0.1.1 released and uploaded to Fiji update site. Release Notes: github.com/mastodon-sc/ma… Update Site: sites.imagej.net/Mastodon-DeepL… Demonstration of functions: youtube.com/watch?v=kQakhh… Mastodon-DeepLineage now belongs to the managed update sites.

#HackPrague24 is underway 💻 this time in Prague! On 15-24 April we are focusing on improving Java-based biomedical image processing SW, in particular Fiji, BigDataViewer, and others 🔍 IT experts, common challenges, and innovation for science!

Stefan Hahmann Constantin Pape Fiji ChatGPT Carlos García If you need a second AI-opinion (😅): I asked gpt-4o and gpt-4-turbo a bit more systematically (n=25). Both seem to agree there are about 54 blobs. Such a quick test costs about $0.40 btw. 💸 haesleinhuepf.github.io/BioImageAnalys…

Mastodon Deep Lineage 0.2.0 released and uploaded to Fiji update site. Release Notes: github.com/mastodon-sc/ma… Update Site: sites.imagej.net/Mastodon-DeepL… Demonstration of functions: youtube.com/watch?v=5GriMg…

I recently was involved in some installations of ELEPHANT server on Windows machines. I have written my learnings into this blog post: biapol.github.io/blog/stefan_ha…

🔀Tracking features can be clustered if represented via a Labels layer. We have a few notebooks in the repository teaching how to turn tracking features from Mastodon into a format compatible to napari-clusters-plotter here: github.com/BiAPoL/napari-…

Trying out the first (experimental!) release of Mastodon git (0.0.1), which can be used to collaboratively work on Mastodon tracking projects. Installation instructions and tutorials: github.com/mastodon-sc/ma… Psst, the video contains secret hints to the author of the tool.🧐

Finally got around to implement this: 💾I/O utilities for points and surfaces in 3D and 4D in napari🔬 - also partially supports saving feature so your data and tables stay together🤝 ➡️ github.com/jo-mueller/nap…

Kyle Douglass And one more shameless self-advertising read recommendation: If users learn basic programming, developers and users can meet in the middle minimizing total effort. (Fig lic CC BY) Johannes Soltwedel & yours truly. onlinelibrary.wiley.com/doi/10.1111/jm…

woke up this morning needing to digitize a map... so I spent 65 minutes drawing a USGS quad by hand, then 31 minutes with the AI vectorizer. here's an hour of #QGIS condensed into 60 seconds (top: AI, bottom: hand)

New blog post🔬💻! biapol.github.io/blog/johannes_… In our group's latest tutorial, I explain how you can train an Ultralytics YOLO object detection/classification 🔍 model for #bioimageanalysis directly from a dataset on an OMERO server openmicroscopy. Short summary 👇

#OMERO is the go-to place to store and organize large amounts of image data. Its ability to annotate images - even collaboratively - makes a tedious task quite a bit easier. And for #YOLO, we luckily only need bounding boxes🖼️, anyway.

Which means, that we just need to clone a dataset, read out the annotations and reformat the bounding boxes and reformat them slightly (#OMERO ➡️#YOLO format) - and that's it, you're ready to train.

The results can be moved directly back to #OMERO using Erick Ratamero's amazing #ezomero . Super-helpful in one-shot detection &classification tasks (e.g., #smartmicroscopy). Data is available CC-BY 4.0: zenodo.org/records/133291… for you to reproduce. Looking forward to feedback!🌻

Assume you have access to the best LLM/AI for #BioImageAnalysis code generation: What would you ask it to code for you? 🙃 Please post your prompt below! Your input will become part of a public dataset shared under CC-BY 4.0, you will be acknowledged. #crowdsourcing Please RT. 🙏

#PoLComic Exploring Science with Physics of Life Dresden: a concept used in the Physics of Life in a comic strip for you! And today: Mass vs Surface Area 1/3: