Cell segmentation tool

Short instructions

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:

  1. Specification of the source images.


    Locate the „Input files“ section and add image files with the „+“ button.

  1. 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“.

  2. 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“.

  1. 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.

  2. 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.

  3. 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.