2020-06-09

Attending: Dom, Seb, June, Petr, Frances, Mark, Melissa, Will, Josh, Wilma, Andreas, Jason, Jean-Marie, Chris

Start: 2:00 pm

1. Accepting minutes from last meeting

N/A

1. Project Status

(2-3 minutes each)

• IDR

  • Frances: good. Working on next release (3 datasets in testing).

    • Josh: should be first release back on EBI Embassy

• SA (learning/mail)

  • Mark: Google Groups looking promising, offering archiving and

    moderation.

    • Can subscribe users without them receiving mail, useful to

      let automated systems submit notifications to list.

    • Can coax subscription lists out of necromancer’s Mailman by

      unpickling list config and can bulk-subscribe in Google.

    • Can fake list submissions without needing MX record

      switched.

    • Any final objections?

    • Seb: migration timelines and any need for testing?

      • Mark: still polishing the expected migration plan, get

        procedure in place then circulate for feedback. Some list specificities need to be accounted for

      • Have other people joining for testing might come next

• Glencoe

  • Chris: bioformats2raw and raw2ometiff issues. Might need to

    write tutorials next.

    • Josh: material available. Question is where does it live

      given both repositories.

    • Chris: considering single external location.

    • J-M: NGFF workshop guide migration? Josh: primarily waiting

      on the renaming.

    • J-M: also more and more material specific to IDR

• Community

  • Jason: Community Survey went out yesterday. Responses largely

    positive. Appreciative of the work. Lots of feedback. Do not edit!

    • Remote aspect of the meeting was very much appreciated

    • Looking forward to the future (still to be defined)

    • Missing in-person discussion

  • Grant reviews available. Overall positive and acknowledging

    great work.

1. AOB

(5 min. max; tech. Discussion should be highlighted to relevant people and rescheduled)

1. Dundee ongoing WFH arrangements.

2. Main Topic

(20-25 minutes plus 15 minutes questions max)

• Jason: points to more general directions.

  • Good response to new data vessels & workflows.

  • Opportunities to bring this forward e.g. import

  • Also metadata for correlative imaging, storing ROIs etc

  • Moving into Summer with decreased team velocity (annual leave)

  • Continue the trajectory of NGFF started in April. Metadata

    specifications

• Josh e.g. what if ROIs are no longer in the DB? How does that affect

  our APIs like the iviewer issue above

  • Start from IDR datasets, store ROIs in Zarr and use this define

    new APIs

  • J-M: also applies to results generated for an image e.g. Ilastik

    probability maps

• Jason: IDR datasets are great use cases for exercising these

  directions

  • Could we get all behind getting data imported in IDR? Distribute

    datasets?

  • E.g. idr0081 (adenovirus) has lots of interesting metadata that

    could be used e.g. for parade

• J-M: feedback from workshop also pointed towards making short videos

  available (<20min)

  • Jason: appreciation of video content for the meeting (despite

    timing & accessibility issues)

• Josh: discuss IDR datasets post standup? Similar process to what

  happened while discussing the conversion of 7 specific images ahead of the meeting

  • Possible topics: rendering, acquisition, plate, ROIs,
• Will: Follow-up discussion on linking to ROIs in iviewer

  https://github.com/ome/omero-iviewer/issues/308

  • For single-shape ROI use case, open the image, left-hand panel

    does not change (full image thumbnails, images in dataset and/or well)

  • How to construct the query with other parameters

    • Generally scalability problem with creating a URL after

      selecting N ROIs

    • Jean-Marie: question of sharing the same view e.g.

      resolution level

    • Jason: are ROIs transmitted when clicking on viewport

      settings?

    • Josh: example of COVID datasets (single ROIs for each

      figure).

    • Chris: similar exposure with Pathviewer. Quickly get into

      weeds when replicating what’s in the UI esp. When considering active/inactive

    • For single ROI case, capturing viewport is a good

      workaround. Does not solve the bigger issue

    • In pathviewer either show viewport or link to ROI and do not

      allow configuration

    • Will: main thing remaining is the control of the Zoom. Seb:

      expand zoom level using bounding box of the ROI

  • Multiple ROIs?

    • Chris: do not allow unless you are ready to explain why some

      of them are not showed

    • Current implementation with multiple ROIs queries all images

      associated with each ROI and displays them in the left-hand panel

    • J-M: issue of creating duplicate thumbnails

    • Jason: would not break thumbnail/image paradigm in left-hand

      panel

    • If multiple ROIs are part of the same image, this loses the

      ability to see all the selected ROIs at once

    • Petr: cf feedback from EDI workshop with similar requests,

      interested in group of ROIs. Chris: built Pathviewer grid with that use case in mind, took > 1 year. Very hard to build generic solutions that are application-agnostic

    • Jason: not even thinking how this would scale in the HCS

      domain

  • Seb: might need to solve 1 ROI/N shape problem

    • Josh: do it iteratively, i.e. get rois=xxx first then

      shapes==xxx

    • Will: effectively the implementation is working on shapes at

      the moment

    • Chris: Support both URLs styles when selecting object

    • When selecting a ROI, return rois or shapes?

  • Petr: question of shape propagation through Z

    • Jason: important but separate question. People in need for

      this functionality.

    • Chris: concepts around multi-shaped ROIs very loosely

      defined.