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# System prepended metadata

title: '2023-08-22'
tags: [Tuesday]

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---
tags: Tuesday
---

# 2023-08-22

Attending: Will, Josh, JM, Dom, Frances, Khaled, Jason, Melissa, Andreas, Kevin, Kyle, Emil, Maadhav  

Start: 2:00 pm UK

## Accepting minutes from [last meeting](https://hackmd.io/team/ome?nav=overview)

## Project Status

(2-3 minutes each)

- IDR (Frances):
    - 2 new studies 139, 149 released last week
    - working towards software upgrade for NGFF
    - Conversions nearly done
    - Some historical fixes needed: idr0004 and idr0010
    - Will: backlog on the BIA side. mostly incomplete studies (only 2-3 studies complete)
    - https://uk1s3.embassy.ebi.ac.uk/bia-integrator-data/pages/test_zarr_pipeline.html 
    

- OMERO
  - omero-insight 5.8.2 release last week - bump Bio-Formats
  - ongoing work on certificates (GS - Seb)
      - doc upgrade and full stack upgrade
      - CENTOS7 connection issues (e.g. from Ubuntu 22.04) doesn't need full stack upgrade - server side only
      - TLS update - need server and client updates

- Bio-Formats (Melissa)
    - NA

- NGFF
  - Java fun: bftools and update sites (Josh)
      - Workshop prep - OME-Zarr support not easy in standalone Bio-Formats.
      - Also https://forum.image.sc/t/getting-started-with-ome-zarr-in-java/85333/3 blosc, QPath etc.
      - Documentation could be improved
      - blosc not available on maven, needs env variable
      - Needs to be usable by regular users, not just devs
      - Josh: created tickets
      - Do we ship s3 support? (currently stripped out)
          - old libs and didn't work with OMERO
      - Seb: auth etc on s3 is hard - restrict scope
  - Will: tables spec - any updates?
  - Warwick:
      - Rajpoot lab repo: https://github.com/TissueImageAnalytics
      - API for H&E models, including HoverNet segmentation: https://github.com/TissueImageAnalytics/tiatoolbox
      - WSI file converter, including support for writing OME-Zarr and DICOM WSI, allegedly 10-100x faster than bioformats2raw: https://github.com/John-P/wsic

- GerBI
    - RDM4mic https://gerbi-gmb.de/activities/rdm4mic/ starting again
    - NFDI - EOSC discussions

- Glencoe
    - Kevin: will start to look at Shape stats...

- Community

## AOB

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

## Main Topic

(20-25 minutes plus 15 minutes questions max)
