---
# System prepended metadata

title: IDR-NGFF 2020-W42
tags: [NGFF]

---

---
tags: NGFF
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# IDR-NGFF 2020-W42

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## 2020-10-16

### Clients
- Josh: additions to the Trevor notes (side problem of a chat solution)
- Will: next client-side thing
  - assuming open with is working
  - assuming Z/T working
  - back to napari? need data, so omero-cli-zarr for one of the specs?
  - looked at grid layout. Lays out channels in a grid. Could possibly use the methods.
  - best solution may be a pyramid with a plate at the top-level
  - or open a new window?
  - is the goal sliders for the whole plate?
### Microservices
- nothing new on micro-services
### Datasets
- Dom: start converting one plate from idr0033 using omero-cli-zarr + option 3
    - Seb: proposing to convert https://idr.openmicroscopy.org/webclient/?show=plate-5966 ( 41744_illum_corrected of idr0033)
- Josh: registered volumes?

### Format
- Tischi opening a Java version of [n5+cloud issue](https://github.com/zarr-developers/zarr-python/issues/540)
    - see https://github.com/BIOP/bigdataviewer-bioformats
    - other metadata specs
        - voxel size as a priority
        - segmentation table 
    - main issue: impossibility to talk to Zarr AND S3 at the same time.
        - Ongoing discussion with Saalfeld et al.
        - If working, could be a candidate library
- Could use/test Zarr reader with BIOP aka BDV + BF
    - Also possible MOBIE (more complex project)
- David: started writing some code for reader
    - test various libraries. Seb: service?

### Summary of next steps
- 

## 2020-10-12

Attending: Will, Seb, Dom, J-M, Josh, Frances, Petr, David, Simon

### Clients

- Will: was fixing open with plugin to handle callback to see if something is enabled
    - make things work in right-hand-panel
    - Josh: blocker on vizarr side?
    - Unclear what the status of vizarr/imjoy
    - imjoy: have been managing to do ImageJ in browser + pulling data from Zenodo
        - main question is: have they handled Bio-Formats? Apparently not yet. Planning to add a few plugins
        - Trevor implemented browser-viewing via Zarr, Imjoy
        - Also can have a talk with Trevor re JS server
        - Simon: propose him to demo at a Tuesday meeting?
        - Josh to invite him in for a meeting in the next 3 weeks

### Datasets

- idr0033 original segmentations
    - Seb: as soon as prod90 is up, will add the segmentations.

- idr0033 notebooks
    - J-M: stripped a lot from existing pipeline. Combines analysis + QC. Removed modules looked for non-existing data
    - Generating CSV files rather than saving into the DB
    - Running other pipeline to see what's happening

### Format

- HCS specification - https://github.com/ome/omero-ms-zarr/issues/73
  - Good reviews
  - Possible issues with many items per group
  - See new option-3 combining all the suggestions
    - 5 layers of folders
    - With largest current screens, 500 elements per folder would be max
    - Current OME metadata fields: https://github.com/ome/omero-ms-zarr/issues/73#issuecomment-705627752
  - J-M: will need HCS-specific client visualization able to handle grid distributed images
      - Josh: short term, assuming new JS and/or napari
  - J-M: how to link redundant metadata for HCS e.g. rendering settings
  - Simon: envisaging "3D" plates? Splitting wells into rows/columns imposes 2D structure
      - Josh: C. Tischer et al interested in other layouts. N. Kiaru talking about using SVG to layout things at arbitrary location (see [NGFF-EMBL-HD-2020-10-02.md](./NGFF-EMBL-HD-2020-10-02.md))
      - If we need hexagonal plate, that's a separate route
  - Seb: assuming we will pick a first layout by end of the week and start hammering it

### Microservices

- https://github.com/manics/docker-example-omero-microservices works!
    - problem in configuration file: one port is integer, the other one is a string
    - Chris will look at cleaning the errors
- next steps?
    - generate thumbnails from Zarr?
    - J-M: assuming thumbnails are not stored in Zarr. Reading binary and generating on-the-fly
