---
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