Mastodawn

Joel Lüthi Oct 24, 2024

It's great to be at #I2K2024 #i2k and see all the other people in bioimage analysis.
If you're interested in OME-Zarr or what we're doing with Fractal, stop by my poster today! :)

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Joel Lüthi Aug 23, 2024

The hackathon is organized by the BioVisionCenter (@vuhlmann , Lorenzo Cerrone, Ethel Mendocilla Sato & me), @joshmoore , Christian Tischer from EMBL, CEITEC's Vladimir Ulman, @normanrz & @perlman

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Joel Lüthi Aug 23, 2024

This year, the hackathon will happen in the context of the Zarr V3 transition and how we best manage this. Main topics will include OME-Zarr in Java, OME-Zarr in the Python ecosystem, OME-Zarr workflows & more. Learn more about the program here: https://biovisioncenter.notion.site/OME-NGFF-Workflows-Hackathon-2024-dde32a032adf49b4a53b4b014586b678

We have structured the hackathon to have 3 core days from Tuesday - Thursday, with the option to attend a (TBD) Monday afternoon program & an extra hacking day for Friday for super motivated people.

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OME-NGFF Workflows Hackathon 2024 | Notion

Date: November 18th - 22nd (core hackathon days are November 19th - 21st)

Joel's Notion on Notion

Joel Lüthi Aug 23, 2024

I'm very excited to announce the #OME_NGFF_workflows_hackathon for November 18th - 22nd at the BioVisionCenter in Zurich, Switzerland.
Sign up here: https://ema.uzh.ch/en/register/ome-ngff-workflows-hackathon-2024.html

This event is a follow-up to last year's successful hackathon, where 45 researchers and developers pushed the boundaries of next generation bioimage formats, processing & workflows. Learn more about last year's event here: https://forum.image.sc/t/outcomes-of-the-next-generation-bioimage-analysis-workflows-hackathon/88733

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OME-NGFF Workflows Hackathon 2024

November 18th - 22nd | University of Zurich, Irchel Campus

UZH Event Portal

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Joel Lüthi Feb 22, 2023

And cc the people involved in the Fractal development in the @priscaliberali lab and the Pelkmans lab, especially Gustavo!

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Joel Lüthi Feb 22, 2023

None of that would be possible without the great #OMENGFF community! It's been great getting to know more & more people on this latest #OMENGFF paper. A very special thanks to @joshmoore for coordinating this paper and for all the work on #OMENGFF ! 👏👏👏
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Joel Lüthi Feb 22, 2023

It's amazing to see all the things that have been built on OME-Zarr in the last year! Our contribution to it is Fractal, an open-source software for processing high content imaging data in the OME-Zarr format (currently in an alpha state): https://fractal-analytics-platform.github.io (3/5)

Fractal Analytics Platform

Process high-content imaging data at scale and prepare it for interactive visualization

Fractal Analytics Platform

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Joel Lüthi Feb 22, 2023

One thing that shows just how fast the community is moving: I only learned about #OMEZarr a bit more than a year ago with the Nature methods paper on #OMENGFF, which convinced me that this was the way forward: https://www.nature.com/articles/s41592-021-01326-w
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OME-NGFF: a next-generation file format for expanding bioimaging data-access strategies - Nature Methods

OME’s next-generation file format (OME-NGFF) provides a cloud-native complement to OME-TIFF and HDF5 for storing and accessing bioimaging data at scale and works toward the goal of findable, accessible, interoperable and reusable bioimaging data.

Nature

Joel Lüthi Feb 22, 2023

Super happy that the preprint for the #OMEZarr paper is out now! If you want to know where bioimage analysis is going: I think this will be the direction! Standardization & open source for the win!

Find the #bioRxiv preprint here: https://www.biorxiv.org/content/10.1101/2023.02.17.528834v1

And Josh's main thread about it here: https://fediscience.org/@joshmoore/109904124384328635

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Joel Lüthi Feb 22, 2023