This plug-in measures a (increasingly) large number of descriptors from the Regions Of Interest (ROI) in the opened images, and export these measures to a text or spreadsheet file. It currently has two working modes:
- Standalone interface: the plug-in will generate a spreadsheet view with one sheet per opened image.
- Via Protocols: the corresponding block will generate a spreadsheet with a single sheet named "ROI Statistics", which can in turn be saved to disk using the "Workbook to file" block (this latter block offers an additional option to merge files together when processing files in batch).
This plug-in is able to save the data in 2 formats:
- Spreadsheet: this option will produce a ".xls" file, compatible with most spreadsheet software. In this format, the ROI color will be used to fill the background of the cell containing its name (NB: the stored color may differ slightly from the actual ROI color, due to XLS format restrictions on color palettes).
- Text: this option will produce a ".txt" file, where each cell is delimited with a tabulation character ("\t"), so as to be easily read by many other software. Furthermore, the name of each sheet will be inserted inside the text file before the actual sheet contents, with beginning and ending "==" symbol (e.g. "== ROI Statistics ==").
- Dataset: the name of the dataset (typically the name of the image or sequence)
- ROI: the name of the region of interest (this can be changed from the "ROI" panel in the Insepctor window)
- X, Y, Z: the coordinates (in pixels) representing the center of the bounding box
- Box width, height, depth: the size (in pixels) of the bounding box along each axis
- Contour: the perimeter (in 2D) or surface area (in 3D), expressed in pixels
- Interior: the area (in 2D) or volume (in 3D), expressed in pixels
- Sphericity (as defined by H. Wadell in 1935): the normalised ratio between the contour and interior, expressed as a percentage (100% for a circle or sphere).
- Roundness (following the ISO 1101 standard): the normalised ratio between the radius of the minimum inscribed and largest cicrcumbscribed circles (or spheres), expressed as a percentage (100% for a circle or sphere). This measure is somewhat similar to the sphericity measure, but it much more sensitive to small shape variations (it is used in the manufacturing industry to guarantee the roundness of "round" objects)
- Convexity: the ratio between the volume and the volume of the smallest convex envelope containing the ROI, expressed as a percentage (100% for a convex object)
- Max. Feret diameter: the maximum distance between any 2 points of the surface, expressed in pixels.
- Major (or first), Minor 2D (or second), Minor 3D (or third) diameters: the diameter (along each axis) of the best fitting ellipse (or ellipsoid), expressed in pixels. They are always ordered such that Major > Minor 2D > Minor 3D.
- Elongation factor: a scale factor given by the ratio between the first and second ellipse diameters (see above). The minimum value is 1 (for a non-elongated object).
- Flatness factor (3D only): a scale factor given by the ratio between the second and third diameters (see above). The minimum vaue is 1 (for an object with perfectly circular section perpendicularly to the major axis)
- Intensity statistics: minimum, average, maximum, sum, and standard deviation of the intensity distribution in all channels inside the ROI
The maximum number of ROI that this plugin can currently handle is 65536 (strange number equal to 16th power of 2). This limit is imposed by pre-2010 Excel spreadsheets.