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ROI Table

A ROI table defines regions of space which are axes-aligned bounding boxes in the image space.

ROI tables can be used for several purposes, such as:

  • Storing information about the Microscope Field of View (FOV).
  • Storing arbitrary regions of interest (ROIs).
  • Use them as masks for other processes, such as segmentation or feature extraction.

Specifications

V1

A ROI table must include the following metadata fields in the group attributes:

{
    // ROI table metadata
    "type": "roi_table",
    "table_version": "1",
    // Backend metadata
    "backend": "annadata", // the backend used to store the table, e.g. "annadata", "parquet", etc..
    "index_key": "FieldIndex", // The default index key for the ROI table, which is used to identify each ROI. 
    "index_type": "str", // Either "int" or "str"
}

Moreover the ROI table must include the following columns:

  • x_micrometer, y_micrometer, z_micrometer: the top-left corner coordinates of the ROI in micrometers.
  • len_x_micrometer, len_y_micrometer, len_z_micrometer: the size of the ROI in micrometers along each axis.

Additionally, each ROI can include the following optional columns:

  • x_micrometer_original, y_micrometer_original and z_micrometer_original which are the original coordinates of the ROI in micrometers. These are typically used when the data is saved in different coordinates during conversion, e.g. to avoid overwriting data from overlapping ROIs.
  • translation_x, translation_y and translation_z, which are used during registration of multiplexing acquisitions.

The user can also add additional columns to the ROI table, but these columns will not be exposed in the ROI table API.