---
# System prepended metadata

title: '2021-01-19'
tags: [Tuesday]

---

---
tags: Tuesday
---

# 2021-01-19

Attending: Will, Petr, Frances, Jean-Marie, June, Simon, Josh, Wilma, Jason, Melissa, David, Andreas, Kevin, Chris

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
  - prod92 - HPA etc ready, all on schedule
  - redmine new server
- NGFF
  - [3D](https://github.com/ome/ome-zarr-py/pull/71) (PR): ready to start downsampling. Viewer ready? 
    - Will: viewer seems to be working, but might be loading lower resolution info. Seen that effect before. 
    - But generally seems to be working (not broken) though not ideal. Confusion about the Z slider giving the same data.
  - [Indexing](https://openmicroscopy.slack.com/archives/C0K5EED3R/p1610987349108800) (slack): 4DN project interested in using [tabix](https://samtools.github.io/hts-specs/tabix.pdf) format, general cross-indexing requirements (along with updating said indexes)
    - How to handle updating of index?
  - [Conversion](https://docs.google.com/drawings/d/1PpB46CGXySQzJqOkdApvSRYn0eSBeZ1fLURPy1VlLO0/edit) (gdraw): EOSC/BBMRI project has similar requirements to our own "zarrification" of IDR.
    - Convert 20-40 TB into OME-Tiff or OME-Zarr
    - Convert on the fly? We don't have solution for this (yet). Do we even want to?
    - Jason: select subset of data and run workflow on. Not permanent.
    - Josh: their usage includes clinical non-image data.
    - Where to keep the state for what's converted?
  - [Collections](https://forum.image.sc/t/ome-ngff-combine-multiple-images-into-one-dataset/47619/13) (imagesc): perhaps some part of this would be good to roll into v0.2.
    - Josh: might be json_ld (breaking)
  - Paper: feedback still welcome!
    - [Current draft](https://docs.google.com/document/d/1loIsB036iGqxgCnUzCWx7bErv-gQvKPfHvVVbXoc36M/edit)
    - Feedback welcome
    - Need 'cost of PFF over time' figure
    - incl. [ngff-latency-benchmark](https://github.com/ome/ngff-latency-benchmark) (GH) currently focusing on TIFF v. HDF5 v. Zarr
    - cf. [aicsimageio benchmark](https://github.com/AllenCellModeling/aicsimageio/blob/master/scripts/benchmark.py) (GH) which doesn't _yet_ test HDF5.

- Releases
  - Josh: omero-py soon
  - JM: TODO: bump omero-py version in other deps

- SA:
  - Simon: ansible roles automatically for galaxy

- Glencoe
  - Chris: ongoing: publication CLA assistant

- Community
    - On-going prep for GBI (IDR workshop) 
    - Connections with protocols.io
      - Emma Ganley - CZI funded.
      - Aims to caputre all experimental details
      - Several journals working with them to provide protocols for papers
      - e.g. IDR dataset link to protocols.io
      - and/or ngff link to protocols.io
      - JM: protocols have searchable keywords
      - Accessible via API. e.g. from ITR

## AOB

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

## Main Topic

(20-25 minutes plus 15 minutes questions max)
