NGFF 2020 Newsfeed

Things appeared to have quieted down over the holidays, but lest the impression arise that nothing’s going on, I thought I’d post a newsfeed from my side (think: “twitter-via-image.sc”) to summarize recent events. If anyone else has news, questions, thoughts or ideas about the future of bio imaging formats, feel free to post below.

~Josh

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“ome-ngff” tag usage

Until another name solidifies, we’ll be using the #ome-ngff hashtag for updates about next generation file formats. Feel free to follow along or create new topics to ask questions.

#new-tag #ome-ngff

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Metadata presentations at SWAT4HCLS

@norio.kobayashi, @sukunis (in absentia), @Caterina and I presented recently at a metadata conference in Edinburgh, discussing a framework for community extensions to the metadata model. The paper should soon be included in the proceedings online, but until then, the slides are on figure.

#community #metadata

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Conversations around standardization

Petr Holub (BBMRI-ERIC) organized a series of calls, which @Caterina , @j.burel and I have attended, regarding the potential inclusion of OME metadata for optical microscopy in an ISO/TC 276 Biotechnology standard draft.

#metadata #standards

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Zarr community meetings

Though it took a few starts, the regular zarr/n5 community meetings are back on the calendar biweekly. The next call is on the 12th of February at 2000 GMT. If you have a topic to raise or would like to be added to the calendar, please speak up.

This week, Zarr’s recent membership in NumFOCUS was discussed, and both @heeler and Jackson Brown joined to discuss various use cases for converting #czi files at the Allen.

#community #meetings #zarr #n5

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OME-TIFF Conversion tools

ICYMI: @melissa posted about a new suite of tools from Glencoe that uses zarr/n5 as an intermediate format for speeding up the transformation of proprietary file formats into pyramidal OME-TIFFs. Feedback welcome.

#ome-tiff #pyramids

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Multiscale arrays (i.e. pyramids) proposal

As a cross-over result from having OME & Zarr at the recent EOSS meeting along with input from @jni, @sofroniewn, and others, I’ve written up a first micro proposal (extension, specification, etc) – https://github.com/zarr-developers/zarr-specs/issues/50 – for initially capturing multiscale (“pyramidal”) arrays. Feedback welcome.

#pyramids

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Metadata presentations at RIKEN

I presented at the RIKEN open science symposium/hackathon on our metadata efforts (cf. NGFF 2020 Newsfeed) Slides are available at https://downloads.openmicroscopy.org/presentations/2020/RIKEN/

With thanks to @norio.kobayashi and the other RIKEN hosts.

#community #metadata

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Multi-scale image labels v0.1

A new specification which is the result of quiet rumblings over the summer has been published: Multi-scale image labels v0.1 which builds on top of the previous multiscale work.

#pyramids #convention