The MorphologyAnalyer2D operator implements a large collection of features to characterize the shape of image regions.
The MorphologyAnalyzer2D is currently under active development. Some of the features already documented below will become available in the next version 1.8.6 of MiToBo which is to be released soon.
Name of Plugin/Operator
- extracts a large collection of features to characterize region shape and morphology
- handles different types of input, i.e., label images and ImageJ ROIs
- optionally provides visualization of extracted features
To run the MorphologyAnalyzer2D perform the following steps:
- install MiToBo by following the instructions on the Installation page
- run MiToBo and start the operator runner by selecting the menu item MiToBo Runner from Plugins -> MiToBo
- in the selection menu navigate to 'de.unihalle.informatik.MiToBo.features' and select the operator MorphologyAnalyzer2D
This will bring up the operator window of the MorphologyAnalyzer2D.
- Input data:
The operator supports two different types of input data:
- label image: an image where for each region the pixels are expected to be uniquely labeled, i.e. all have the same intensity value; all pixels being labeled with 0 are treated as background
- regions (in ImageJ ROI format): here regions can directly be imported from ImageJ's ROI manager or be read from ROI files in specific formats from disk; also manual input of region data is supported
- Calibration information:
Many of the features refer to measuring lengths or areas of region entities. The units to be used for these measurements can freely be configured.
If appropriate calibration data is available from the given input data, e.g., as meta information in a label image, this data is automatically used and displayed.
But, the user can overwrite the calibration by manually specifiying the size of a pixel in the desired units.
E.g., with regard to microscopy images a common unit are microns and a proper calibration requires to provide information on the size of a pixel in microns.
The operator always assumes square pixels, i.e. the pixel lengths in x and y dimension are assumed to be equal.
If this does not hold for an image or ROI data some of the feature values will be incorrect!
Lengths are first measured in pixels by the operator and areas in square pixels. Subsequently the numbers are then converted to the specified units, e.g., converted to microns or square microns based on the given size of a pixel.
- Configuration of features to calculate:
The configuration window allows to select and configure the set of features to be extracted:
|Name of Option||Description|
|Calculate area||activates area calculation; area is measured in terms of the number of pixels in a region|
|Calculate perimeter||activates perimeter calculation; the region perimeter is calculated from the 8-neighborhood contour of the region; the contour is extracted and then traced where each horizontal or vertical step yields a distance of 1 and each diagonal step a distance of √2; the final perimeter is given by the sum of the distances between every pair of neighboring pixels along the contour|
|Calculate length and width||activates calculation of length and width; to eactract length and width of a region an ellipse is fit to the region pixels; two times the length of the major axis defines the length of the region, two times the length of the minor axis defines its width|
|Calculate circularity||activates calculation of circularity; circularity is given by <math>x^2</math> 4 * * this.area) / (perimeter * perimeter) which the result files and intermediate data is written|
|Calculate margin roughness|
|Analyze protrusions and indentations|
|Calculate skeleton branch features|
|Calculate concavity information|
|Calculate convex hull measures|
|Show curvature analysis info image?|
|Show skeleton analysis info image?|
|Verbose||turns on output of additional debug messages; the messages are shown in the console|