--- 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.