Datasets

Supported dataset formats

Container formats

• webknossos-wrap (WKW). Optimized format for large datasets of 3D voxel imagery. Supports compression, efficient cutouts, multi-channel and several base datatypes (e.g., uint8, uint16).
• KNOSSOS cubes. Dataset of 128x128x128 cubes.

Image formats

• Grayscale data (uint8), also referred to as color data
• RGB data (24 Bit)
• Segmentation data (8 Bit, 16 Bit, 32 Bit)
• Multi-channel data (multiple 8 Bit)

Tools

Of course datasets do not need to be created manually. The webKnossos cuber converts image stacks and KNOSSOS cubes into a WKW dataset. It also compresses datasets for efficient file storage and creates necessary metadata.

Dataset file structure

WKW dataset

test_dataset           # One folder per dataset
├─ color               # Dataset layer (e.g., color, segmentation)
│  ├─ 1                # Magnification step (1, 2, 4, 8, 16 etc.)
│  │  ├─ header.wkw    # Header wkw file
│  │  ├─ z0
│  │  │  ├─ y0
│  │  │  │  ├─ x0.wkw  # Actual data wkw file
│  │  │  │  └─ x1.wkw  # Actual data wkw file
│  │  │  └─ y1/...
│  │  └─ z1/...
│  └─ 2/...
├─ segmentation/...
└─ datasource-properties.json  # Dataset metadata (will be created upon import, if non-existant)

Sample datasource-properties.json:

{
  "id" : {
    "name" : "test_dataset",
    "team" : "<unknown>"
  },
  "dataLayers" : [ {
    "name" : "color",
    "category" : "color",
    "boundingBox" : {
      "topLeft" : [ 0, 0, 0 ],
      "width" : 1024,
      "height" : 1024,
      "depth" : 1024
    },
    "wkwResolutions" : [ {
      "resolution" : 1,
      "cubeLength" : 1024
    }, {
      "resolution" : 2,
      "cubeLength" : 1024
    } ],
    "elementClass" : "uint8",
    "dataFormat" : "wkw"
  }, {
    "name" : "segmentation",
    "boundingBox" : {
      "topLeft" : [ 0, 0, 0 ],
      "width" : 1024,
      "height" : 1024,
      "depth" : 1024
    },
    "wkwResolutions" : [ {
      "resolution" : 1,
      "cubeLength" : 1024
    }, {
      "resolution" : 2,
      "cubeLength" : 1024
    } ],
    "elementClass" : "uint32",
    "largestSegmentId" : 1000000000,
    "category" : "segmentation",
    "dataFormat" : "wkw"
  } ],
  "scale" : [ 11.24, 11.24, 28 ]
}

Import datasets

Use the upload function in webKnossos:

• Recommended only for smaller datasets (max. 1 GB)
• Create a zip-file of dataset as specified above

File-system import:

• Place the dataset at <webKnossos directory>/binaryData/<Organization name>/<Dataset name>
• Wait for webKnossos to detect the dataset (up to 10min)
• Go to the dataset view on the dashboard
• Click Import for your new dataset
• Review, correct and approve the dataset metadata. Usually, scale and largestSegmentId needs to be set manually.

Comparison to KNOSSOS

KNOSSOS datasets can be reused in webKnossos with slight modifications:

• The folders of the magnification steps have a different naming scheme: mag1 → 1, mag2 → 2
• webKnossos compatible metadata needs to be created (i.e., datasource-properties.json). knossos.conf can not be used directly.
• Make sure to put each dataset layer into its own directory structure (e.g., color, segmentation)
• Compressed KNOSSOS cubes are not supported. Please convert to WKW for compression support.