Upcoming calls on next-gen bioimaging data tools (Starting Oct. 29)

There are now a few people working on short, pre-recorded presentations along the lines of @perlman’s lightning talk suggestion. If anyone else would like to record themselves going over 2-3 slides (and/or application demo) in 5 minutes or so, I’ll get them all stitched together and uploaded next week. If you’re interested, drop us a line:



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@joshmoore I would be really interested to participate in this too!

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Dear All
In case THE METADATA FOR NGFF topic interests you I have initiated a dedicated TOPIC that can be found here:



Is it too late to be registered ? :slight_smile:

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Not at all. I’ve added you to https://forum.image.sc/t/connection-information-for-next-gen-call-on-oct-29th/44210 . If anyone else needs adding (or worse, has not received the notification for that direct message), please let me know.

All the best,

Also, if anyone is still looking to submit a short lightning-style talk (~5 minutes), I really should have them early European Wednesday in order to get them linked and available to everyone.

Feel free to show code or demonstrate code and/or data, including roadblocks you’re facing, which can help to shape the discussions.

If you are posting them publicly, feel free to link here. Otherwise, get in touch via https://forum.image.sc/new-message with info on how I should download them.

All the best and see you Thursday,

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Tomorrow’s the day. And though a talk or two more may still trickle in, I thought it best to post the few videos I’ve received so that all of our timezones have roughly a full day to watch them.

A few points:

  1. If you didn’t manage to film a lightning talk, don’t sweat it! These calls aren’t meant to add to our existing stress levels, but let us work together more efficiently. (And there’s always a chance next time.)
  2. If you still want to record one, go for it! Think of it as saving us time for more in-depth discussions. Send a link or a file and I’ll update things as necessary.
  3. If you haven’t yet, check out the brainstorming document linked from the connection page and add any topics that you may want to discuss.

Without further ado…

Lightning talks

Name Video Length Size Materials
Josh Moore NGFF Timeline Recap 6:56 12M hackmd
Will Moore OME-Zarr Plate Clients 5:43 11M
Chris Allan OMERO Plus, PathViewer and NGFF 4:16 30M
Trevor Manzt NGFF & Viv (youtube) 5:20 43M


P.S. Yes, I went over 5 minutes. I’m the worst.


I’d love to participate, so can I get registered?


I’m interested as well!


I would like to register too, if its not too late!

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Update: added a video from @manzt!

@joshmoore would love to get added.

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@joshmoore I’d like to be added as well!

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@joshmoore I would like to participate as well, thanks !

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I’d like to join as well!

Sorry, @rchhetri, I didn’t get your request until the meeting had already begun. Next time!

Otherwise, That’s a wrap!   :clapper:

Thanks to the 4 dozen or so of you who joined over the course of the day. (Some joined twice, so thanks 2x.) I’ve locked the meeting notes but they are public if anyone who couldn’t attend wants to take a look. The recordings are currently being uploaded, and I’ll update this thread once they are in place.

A summary write-up of the main conversations like:

  • What is “ngff”? :smile:
  • How to deal with many small files?
  • APIs versus file formats
  • sparse versus dense
  • additions to the multiscale & labeled image specs
  • representations for polygons, tabular data, etc.
  • storage of flexible metadata

is certainly in order, but I likely won’t get to it for a week or two. But by all means, if anyone wants to add their thoughts, impressions, or generally keep the conversations going, very looking forward to it. If you start a new topic, add the #ome-ngff tag and those who are interested should be able to follow along.

A few procedural decisions were made regarding how future community calls will take place:

  • In roughly a month, I’ll kick off another similar topic to see if there’s interest in another meeting. We’ll need to keep #i2k2020 in mind for the scheduling.
  • The feeling was that generally organizing the meetings completely within image.sc was successful, but…
  • we need to balance the notification to noise ratio. For example, what’s the best way to let everyone express “I’d like to join”? Suggestions welcome.
  • For everyone who has already expressed interest, I’ll set up an @ngff group in order to more easily give access to the connection information. Thoughts welcome on how else to make use of that.
  • We sadly didn’t choose a better name, so keep your proposals coming! :wink:

Thanks to all for taking time out of your crushing schedules. It was great to see everyone.


Is there somewhere discussion thread for label images and label annotations?
I had some thoughts that I would like to share.

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Shall we stick to Multi-scale image labels v0.1 for the moment? ~J


@joshmoore Responding a little late, but better late than never. Keen to join. Would you add me to the list?

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A final update to this thread:

See some of you at #i2k2020 for Next call on next-gen bioimaging data tools (Dec. 2)