Dataset

A dataset consists of a root directory, which must contain the file dataset.json with a valid dataset schema. It should contain the subdirectories images, containing the image data, tables, containing the table data and may contain the directory misc, containing additional data associated with this dataset. Note that the location of image and table data is determined in dataset.json and it is thus possible to choose a different directory structure than images/ and tables/ to store them, but the layout using images/ and tables/ is recommended for consistency with other MoBIE projects and assumed throughout this document.

The images directory contains the metadata files describing the image data, see data specification for details. It may contain additional subdirectories to organise these files. By convention the files for different data formats are often separated into folders named accordingly, e.g. images/bdv-n5 and images/bdv-n5-s3.

The tables directory contains all tabular data assoicated with segmentation, spot or region sources (see the data specification for details) The tables associated with a segmentation or view, must all be located in the same subdirectory. This subdirectory must contain a default table, which should be called default.tsv, and may contain additional tables. See the table data specification for details on how tables are stored.

The misc directory may contain the subdirectory views with additional views stored in json files according to the views spec.

As an example see the dataset directory structure for the hela dataset of the clem project:

hela/
├── dataset.json
├── images
│   ├── bdv-n5
│   └── bdv-n5-s3
├── misc
│   └── views
└── tables
    ├── em-crop
    └── lm-tomogram-table

Dataset Metadata

The dataset metadata, stored in dataset.json, has the following structure:

• defaultLocation: Default location used to initialize the location GUI element of the MoBIE menu.
• description: Description of this dataset.
• is2d: Are all images in this dataset two dimensional?
• sources: Mapping source names to their specification.
• views: Mapping of view names for to their specification. Must contain the default view.

For example, the dataset.json file for the hela dataset looks like this (source and view metadata omitted for brevity):

{
    "defaultLocation": {...}
    "description": "A correlative electron microscopy sample of a HeLa cell.",
    "is2d": false,
    "sources": {
        "em-detail-a1-A": {...},
        "em-detail-a2-A": {...},
        ...
    },
    "views": {
        "default": {...},
        ...
    }
}