---
# System prepended metadata

title: NGFF-EMBL 2021-01-22
tags: [EMBL, ' NGFF']

---

---
tags: EMBL, NGFF
---

# NGFF-EMBL 2021-01-22

Attending: Tischi, Josh, Constantin, Kimberely Meechan

* CT: Java for writing
  - bioformats2raw as library?
  - raw then to zarr? No. raw is zarr.
  - gradle? Repository URL.
* CT: Java for reading
  - https://github.com/dgault/bioformats/tree/ExternalZarrReader
  - Christian to write his own for BDV
* CP: n5 in bioformats2raw
  - Looking at jzarr. Need something like numpy.
* CT: how to get things onto s3? (from Java)?
  - write & then copy
  - https://github.com/glencoesoftware/bioformats2raw/pull/17 ?
  - https://s3.embl.de/bioim/s3-browser.html
  - job of IT department
  - Also: copying of directories
  - KM: easy way to just write the XML files
  - JM: BIA? National, etc.
  - CT: IT parallelizes
* CT: image collections (mobie context)
  - images.json like a zgroup
  - options:
    - images as keys
    - collection as keys as well with:
      - `"type": "collection"`
      - `"layout": "auto-grid"`
    - drop-down menu based from splitting on "`-`"
    - also have bookmark with the default view
    - _either_ collections _or_ images?? i.e. remove a collection if an image is added. (CP: different coordinate systems)
    - Typically, images in a BDV group would have linked brightness/contrast. Especially important for HTP.
    - CT: BDV as desktop? Bookmark would say open an auto-grid collection and then apply whatever transformation the user wanted.
    - CP: or another layout type `"explicit"`
    - KM: saw that the transforms weren't being saved. Nico/EPFL has something in bdv-playground.
  - CP to update the https://github.com/mobie/mobie/issues/20
  - CT: ok to suggest update to OME-Zarr? JM: Yes!
    - Would avoid a breaking version, but go for it.
    - Would need to get other implementations to implement.
  - CP: can make the next version in OME-Zarr (i.e. mobie native first)
    - CT: COVID as a proof-of-concept
* CT: transforms? Follow COSEM transformations. Can update later.
* CT/CP: do breaking `"."` --> `"/"` 
* CP: 5D C/T dummy? No
  - cf. support for 3D trees
  - CT: chatted with Tobias. Was for lightsheet. Start taking a movie and then the embryo grows larger, then you have to grow larger
  - JM: Good use cases. Complicates the clients. 
  - CT: ilastik is 5D internally. Different philosophy: tries to map everything to 5D.
  - CT: collections of 2D, then metadata per slice....
* Misc
  - ... all adopting tomogram for writing.