---
# System prepended metadata

title: '2023-11-28'
tags: [Tuesday]

---

---
tags: Tuesday
---

# 2023-11-28

Attending: Will, Jason, Dom, Petr, David, Muhanad, Josh, Khaled, Andreas, Melissa, Peter Todd, Erin, Chris, Maadhav, Steve, Tom, Kevin, Seb, 

Start: 2:00 pm UK

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

## Project Status

(2-3 minutes each)

- IDR:
    - NGFF: Some invalid OME-NGFF filesets identified when creating memo files - re-converted and submitted to EBI
    - Some other issues in a small number of images identified by [check_pixels.py](https://github.com/IDR/idr-utils/pull/55). idr0004 image rendering issue. Also 1 invalid duplicate plate in IDR re-converted and re-uploaded to EBI 

- OMERO:

- Bio-Formats:
    - ZarrReader (see above)
    - Bio-Formats 7.1.0 planned to release week of 11th December
        - Release process training - good to have more team members familiar
        - Jason: DICOM PRs? Yes, included

- NGFF (Josh)
  - Transforms PR ongoing. Community keen!
  - Zarr Hackathons (Berlin/Python now, Janelia/Java)
  - NGFF website "help needed" section where community can contribute. 
  - Roadmap for the new year
      - Transforms support in ZarrReader

- GerBI (Tom)
    - KVpairs - webclient and OMERO.figure support for 'parent' KVP annotations
    - Pre-Hackathon - OMERO connection to ARC? https://www.nfdi4plants.de/content/learn-more/annotated-research-context.html
    - KVpairs scripts ongoing. Namespace support and OMERO-guides.

- Glencoe (Chris)
  - OMERO.web PRs opened. 
  - PyTables - looking at cool features of latest versions, slicing & querying
  - Erin: https://github.com/glencoesoftware/omero2pandas/releases/tag/v0.2.0 
  - bioformats2raw release in next few days.

- Community
  - Jason/Josh on NIH Image Data call tonight.
  - Pittsburgh - use-cases discussion.

## AOB

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

## Main Topic

 ### MDV and OMERO-MDV
 
 Steve Taylor, Peter Todd
 - https://mdv.molbiol.ox.ac.uk/
 - https://github.com/will-moore/omero-mdv
 
 - Analytical tools for Chip-seq data, Multi Locus View for genomic data...
 - Led to development of MDV
 - Weeratunga etal Nature Comms.
 - Spatial Omics Oxford Pipeline:
     - Hyperion spatial data. Mass-spec protein analysis per pixel of image
     - Deep Cell - segment images -> cells
     - UMAP dimension reduction -> table
     - Spatial statistics
     - View in MDV
 - MDV - can upload data to portal
 - https://mdv.molbiol.ox.ac.uk/projects/hyperion/6567?view=Sample+information demo
 - Interactive charts
 - Pair-Correlation-Function - cell neighbours 20 microns
 
