ROI Intensities File Format

This page details the file format when ROI intensities are written to disk by the ROI Toolkit of Jim.

An intensities file is a plain text file, consisting of:

• A header line which looks like the following:

    # x y intensity
  

• An entry for every slice that contains ROIs, in the following format.

  • If the check-box for the Slice entry in the ROI Toolkit Dialog is checked, then there is a header for the slice which looks like the following:

    # Slice n

  where n is the slice number (numbered from 1 upwards).

  • An entry for each ROI.

  The entry for each ROI has the following format.

  • If the check-box for the Annotation entry in the ROI Toolkit Dialog is checked, then there is a header for the ROI which looks like the following:

    # Annotation

    where Annotation is the annotation for the ROI.

  • A list with 3 columns and N entries, where N is the number of pixels where at least half the area of the pixel lies within the ROI. Each row has the x coordinate of the pixel's centre, the y-coordinate of the pixel's centre, and the pixel intensity. The x and y coordinates may be either in mm, or in pixels, depending on the setting of the display units.

  • A terminator for the ROI consisting of a single & character on a line by its self.