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Database

Vodex stores the information about the experiment in a SQLite database.

There are the following tables:

  • Image Data TabFiles : stores the filenames relative to the main directory (FileName) and number of frames in each file (NumFrames)
  • AnnotationTypes: stores the types of annotations (Name) and descriptions (Description) which is optional.
  • Frames: links each frame in the experiment to the file (FileId) and a frame in that file (FrameInFile)
  • Cycles: IF the annotation (AnnotationTypeId) was created from a cycle, stores the cycle as a json string (Structure)
  • AnnotationTypeLabels: for each annotation type (AnnotationTypeId) stores the names of the labels (Name) and their descriptions (Description) which are optional.
  • Volumes: links each frame in the experiment (FrameId) to the volume (VolumeId) and a slice in that volume (SliceInVolume)
  • CycleIterations: links each frame in the experiment (FrameId) to the cycle (CycleId) and the iteration of that cycle (CycleIteration)
  • Annotations: links each frame in the experiment (FrameId) to the label (AnnotationTypeLabelId)
  • Options: stores some additional information as a Key - Value pair. Contains the following keys:
    • data_dir: the directory with the image Files
    • frames_per_volume: frames per volume parameter
    • num_head_frames: number of frames at the beginning of the recording that do not form a full volume
    • num_tail_frames: number of frames at the end of the recording that do not form a full volume
    • num_full_volumes: number of full volumes in the recording

See diagram for more details.

You can explore each table in more details using the database for the Toy Dataset. We recommend using a DB Browser for SQLite to explore the database content. It is also a good place to test out your queries if you want to add some functionality to the dbmethods module.