---
# System prepended metadata

title: Zarr resources brainstorming (4)
tags: [NGFF]

---

---
tags: NGFF
---

# Zarr resources brainstorming (4)

Attending: Petr, J-m, Erin, Will, Josh

- URLs
    - Placeholder ready for the paper
    - Take something out of https://ome.github.io/ome-ngff-tools/
    - Tools page:
        - tools for dev
        - move to something more like paper i.e. support t
    - Data page:

# Zarr resources brainstorming (3)

Attending: Petr, J-m, Josh, Erin, Will

- URLs:
    -  ome.openmicroscopy.org/ngff/data
        -  link to IDR and other pages
    -  ome.openmicroscopy.org/ngff/tools
    -  Break-up spec page into pages?
    -  Replace bikeshed with readthedocs? Only use a couple of bikeshed features (internal links, abbreviations)

# Zarr resources brainstorming (2)

Attending: Petr, J-m, Josh, Erin

- Goal today: URLs to send to other authors
  - data hierarchy:
    - central location (TBD):
      - individual catalogs
        - links to bucket, etc.
      - topic-matching repos
        - whatever
  - tool (registry) hierarchy:
    - by-domain (for scientists)
    - by-language (for devs)

- J-m: viewer table is developer centric
  - JM: agreed, guide more verbose.
  - ED: by domain rather than data type.

- Naming
  - JM: bioformats2raw / ngff-converter
    - bioformats
    - bioformats2raw (lib) --> high-performance bioformats? multi-threaded bioformats
    - bioformats2raw (cli) --> bioformats-cli? -writer?
    - ngff-converter --> bioformats-gui
  - ED: "import" sounds like a copy
    - JM: also from the iRODS group. could see having `bin/omero register` (for inplace)
    - ED: even have own importer of NGFF (especially with OMERO and NGFF). opportunity to not rewrite but be explicit.
    - JB: essential to have the naming write
    - PW: even renaming omero import, because it needs massive changes in the documentation
      - you won't get it right the second time
      
- URLs (Erin left)
  - keep URL
  - probably RTD
  - probably more subpages
  - put redirects in place
  - migrate notebooks?

```
SPEC:

ngff.o.org/          ->      ngff.o.org/latest
ngff.o.org/latest    ->      ngff.o.org/latest/spec

DATA:

ngff.o.org/datasets  ->      ngff.o.org/latest/datasets
ngff.o.org/data-resources

possible other terms: data, datasets, catalog, 

TOOLS:

ngff.o.org/tools
ngff.o.org/tool-registry
ngff.o.org/resources/tools -> ngff.o.org/latest/resources/tools

possible other terms: tools, tools-registry, 

NOTEBOOKS:

ngff.o.org/data
ngff.o.org/tools
ngff.o.org/in-action
ngff.o.org/usage
ngff.o.org/notebooks

OTHER PAGES TO CONSIDER:

ngff.o.org/commercial-support
ngff.o.org/commercial-support
https://www.openmicroscopy.org/commercial-partners/#partnerships
https://docs.openmicroscopy.org/ome-model/6.3.1/ome-tiff/index.html#support

https://ome-files.readthedocs.io

https://files.openmicroscopy.org/ome-tiff
https://files.openmicroscopy.org/ome-zarr
https://specs.openmicroscopy.org/ome-zarr
https://specs.openmicroscopy.org/zarr
https://specs.openmicroscopy.org/ome-xml

ngff.o.org/  -> specs.o.org/ome-zarr
OR
tiff.openmicroscopy.org
OR
www.openmicroscopy.org/ome-tiff
www.openmicroscopy.org/ome-zarr

```
* (From Seb): ngff.o.org/about or ngff.o.org/teams or similar

# Zarr resources brainstorming (1)

Attending: Petr, J-m, Josh, Erin

- J-m: https://ome.github.io/ome-ngff-tools
  - focused on viewers.
  - People asking: where to find samples?
  - Where do converters go?
  - Where? github, ngff page, main docs web
  - Other issues: logo, etc. (GS, GerBI)
  - Example of files: 
      - https://uk1s3.embassy.ebi.ac.uk/bia-zarr-test/bia_examples.html
      - https://idr.github.io/ome-ngff-samples/
      
- Erin: paper? landing page?
  - Josh: certainly would be a good output of the paper
  - J-m: also notebooks
  
- Erin: https://www.glencoesoftware.com/products/ngff-converter/ product page
  - could also include import, etc. "state of OMERO Plus"
  - everything else is really in blog posts
- Josh: how do others do it?
  - https://hdfgroup.org/
  - https://dicom4qi.readthedocs.io/en/latest/resources/datasets/
  - https://github.com/marketplace
  - https://www.openmicroscopy.org/ome-files/ 
  
- options
  - ome.readthedocs.io/zarr/tools
  - ome.readthedocs.io/zarr/data
  - or guides.openmicroscopy.org/zarr
  - possibly: github.com/ome/ome-zarr-tools
  - https://github.com/topics/omero-cli-plugin 
  
- table as intersection of tools X data
  - most valuable
  - requires more 
  - Erin: 3d, plates, labels, ...
  - J-m: currently "spec validator"
  
- **progression**
  - blog (timestamped)
    - github table (timestamped)
      - maintained documentation page