All features of the tool may be accessed by the user-interface elements of the main window.
Segmentation and counting of cell in a batch of images can be done in the following steps:
Specification of the source images.
Locate the „Input files“ section and add image files with the
„+“ button.
Files in the list can be selected by the mouse, multiple selections are possible by pressing the „Ctrl“ or „Shift“ button.
Files in the list are processed in the order they appear.The buttons „/\“ and „\/“ allow to change the order of the selected files.
Selected files may be removed from the list by the „-“ button.
Specification of a file name replacement rule for segmented files.
The labelled images are stored in the same directory under
the name of the source image transformed by this rule. E.g,.
the above example yields image.png → image_seg.png.
The output of labelled images can be suppressed by unchecking „Generate labelled images“.
Configuration of the segmentation parameters.
The configuration dialog can be invoked by pressing the
button „Configure...“ in the section „Counting“.
There are default values which can be accessed by the button „Default“.
„Processing images“ switches the segmentation procedure.
„Crop image“ allows to crop the left, right, top and bottom margin of each input image according to the specified values in pixels.
„Scale image“ allows to scale each input image to the specified size in pixels.
„Median filter size“ is given in pixels. It should be greater than the size of relevant features and smaller than size of irrelevant background features.
„Total variation smoothing“ allows for edge-preserving removal of noise from the input image. The regularization parameter and iteration count adjust the level of noise and the accuracy of the numerical algorithm, respectively.
„Segmentation threshold“ specifies how much deviation of the mean value of the filtered image should be considered as a feature.
„Feature size“ specifies the minimal number of connected pixels a segmented region has to possess in order to count as a feature.
Segmentation of the images.
The segmentation can be started by pressing the button „Process files“ in the „Counting“ section.
Progress can be observed in the „Job status“ section.
Generation of the report.
A list containing the number and positions of the counted cells for each image is generated by pressing the „Generate“ button in the section „Report“.
The output file name can be specified in a dialog. The data
is stored as a comma separated list (csv). Each line corresponds
to a single cell and contains the name of the image file, a serial
number and the (x,y) coordinates of the center of mass.
Storage of the parameters (optionally)
All parameters may be stored in a file by selecting „File → Save Job“ in the menu.
They can be restored by selecting „File → Load Job“ in the menu.