N5¶

WEBKNOSSOS can read N5 datasets.

N5 datasets can both be uploaded to WEBKNOSSOS through the web uploader or streamed from a remote server or the cloud.

Examples¶

You can try the N5 support with the following datasets. Load them in WEBKNOSSOS as a remote dataset:

Interphase HeLa cell EM data hosted on AWS S3
- s3://janelia-cosem-datasets/jrc_hela-3/jrc_hela-3.n5/em/fibsem-uint16
- Source: Open Organelle Project

N5 folder structure¶

WEBKNOSSOS expects the following file structure for N5 datasets:

my_dataset.n5             # One root folder per dataset
├─ attributes.json        # Dataset metadata
└─ my_EM                  # One N5 group per data layer. In WK directly link to a N5 group.
   ├─ attributes.json                
   ├─ s0                  # Chunks in a directory hierarchy that enumerates their positive integer position in the chunk grid. (e.g. 0/4/1/7 for chunk grid position p=(0, 4, 1, 7)).
   │  ├─ 0
   │  │  ├─ <chunks>
   │  ├─ ...
   │  └─ n
   ...                
   └─ sn

For details see the N5 spec.

Performance Considerations¶

To get the best streaming performance for N5 datasets consider the following settings.

Use chunk sizes of 32 - 128 voxels^3