---
# System prepended metadata

title: '2021-01-12'
tags: [Tuesday]

---

---
tags: Tuesday
---

# 2021-01-12

## Attending

* Petr, Josh (notes), Frances, June, Simon, Dom, Jason, J-m, Melissa, David, Wilma, Chris, Emil, Erin, Will, Kevin

Start: 2:00 pm UK

## Accepting minutes from [<u>last meeting</u>](https://github.com/ome/meeting-minutes)

## Project Status

(2-3 minutes each)

- IDR
  - Working on next release (ETA: end of January)

- NGFF
  - Downsampling in Z:
    - https://github.com/ome/ome-zarr-py/pull/71
    - Looking maybe into bdv
      - https://javadoc.scijava.org/Fiji/index.html?bdv/export/Downsample.html
  - Leiden & "Federation"
    - various pieces of the puzzle, and we need to figure out where we're investing (oldest to newest)
      - OmeroReader
      - exporter (OmeroMetadata)
      - downloader
      - duplicate
      - omero-cli-zarr
  - Deep zoom
    - Simon: isn't this what Will did with HCS?
    - JRS: there's a difference
    - Chris: disconnect between the preview & the actual data. More than an affine transform. Calculating approximation with computer vision
    - Simon: working towards multimodal viewing
    - JRS: multimodal may be the best way to express it. in digpath, lowres+hires. Alternatively, can place the macro somewhere in the display
    - Josh: with a context box like bird?
    - Chris: file format specific. optimal to have them.
    - Chris: also a question of if you've captured _multiple_ images. (i.e. lots of things)
    - Emil: number of customers in digpath where it's already an issue. Multiple tisse samples from the same slide. Very difficult to know which is which in OMERO. Linkage is important.
    - Erin: agreed. Cute to have the overview but isn't the necessary piece. The mapping is more important. Annotations are essential, especially if it should be a single "canvas"
    - Emil: there is software that treats it like OMERO, other does not.
    - Simon: sounds like ROIs
    - Josh: to some extent, ROIS could just be images.
    - Petr: yes, image image link

- Releases
  - Simon: discussing omero-py release (5.9). Objections?
    - J-m: need secrets to be set up for conda packages. will synchronize with Seb.

- SA
  - [Flash is dead](https://isflashdeadyet.com/) (utterly)
    - i.e. don't tell anyone to upload to QA
    - David: alternative?
    - Josh: zenodo?
      - JRS: downside? Private files.
      - Chris: i.e. publicly available.
    - Simon: see upload_test

- Glencoe
  - Updating bioformats2raw with jzarr.
    - Needs performance testing.
    - Using that from microservices (e.g. during rendering)
  - Using the opportunity to align with ome-zarr layout.
  - JRS: Glencoe contacted by imaging data commons (NCI/IDC)
    - Announced during public presentation 1-2 months ago
    - adding readers/writers for variants of DICOM-WSI
    - specifying the work now, but settling down into a definition
    - Q1-2/2021

- Community (14:28)
    - LIM/Nikon (David)
      - company producing OME-TIFF files that need validating (incl. FileAnnotations with proprietary byte arrays).
      - Tested via import to OMERO and re-export. Import, visualization, and export all need work. Prepared to undertake that?
      - Pondering for a bit before deciding, may need to discuss the overall goal.
      - Open to better suggestions
    - Workshops
      - GBI thread (27-29.01)
      - Stockholm (10.02)
      - McGill (18-19.02)
      - Gothenburg (TBD) - likely to want late Jan/Feb.

## AOB

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

## Main Topic

(20-25 minutes plus 15 minutes questions max)

[2021 Roadmap](https://docs.google.com/document/d/1tlP-hwndsc4yVAkP5g61Xbt-VUGJRW5ciuoWxxvMeJw/edit#)
 - JRS: objections for these high-level activities for the next few weeks
 - Missing: training (Added)
 - Workflows, J-m? Added under various sections
   - Need to decide where we're going to run them.
   - Conversation about what will be exposed as Zarr work.
   - NB: Ice 3.7 may be a problem. S3 could be an alternate route, simplifying the data access.
   - Notebooks are a cross-cutting concern.
 - Simon: docs reoganization?
   - J-m: going back to it now that GitHub Actions are done.
 - JRS: feedback by next week then. :+1: