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
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.
@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.
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
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
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
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
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.
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
@ngff group createdAs discussed during the recent NGFF community call, a @ngff group (or “mailing list”) has been set up in order to more easily send notifications to people who are interested in this topic.
There is now a blog post listing the available images in OME-Zarr, primarily based on Multiscale arrays v0.1 but with one example of Multi-scale image labels v0.1. As we finalize the label specification and move to post the draft HCS specification, we’ll update the blog with more data.
Four or five dozen of us kicked off what will hopefully be a series of community calls regarding #ome-ngff at the end of October. The pre-recorded talks as well as a recordings of the two separate Zoom sessions are available under: https://downloads.openmicroscopy.org/presentations/2020/community-call-2020-10-29/
The next call will be less formal and concurrent with the Images 2 Knowledge meeting next week. Details are available in Next call on next-gen bioimaging data tools (Dec. 2)
Once the year starts to calm down, we’ll start planning the first call for the new year. Ideas and especially pre-recorded talks welcome!
The spec document has now migrated to its own repository:
PRs are welcome to the latest version. See the bikeshed documentation for information about the markdown-extensions that it provides.
The published version of the current editor’s draft (i.e. latest commit) is available at https://ngff.openmicroscopy.org/latest. Released versions are available as suffixes of the form: https://ngff.openmicroscopy.org/0.1
In time for our #i2k2020 workshops, we’ve just posted a second blog post listing the available HCS data in OME-Zarr. Do note (with our apologies) that there’s not yet an image.sc thread for the HCS spec. We simply ran out of time. Coming soon to a forum near you!