NGFF January 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: “”) 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.


“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

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

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

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

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