Expertomica Cell Marker

The software can read the series of images visualize them and allow the user to define the borders of cells

This work was supported and co-financed by the South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses (CZ.1.05/2.1.00/01.0024).


The software was originally developed for manual labeling of cells in series of microscopy images for cell behavior analysis. The software can read the series of images visualize them and allow the user to define the borders of cells. The information about labeled cells is exported into txt file and it can be used for next processing. The software allow the user to do the standard labeling operations (object ID, object replication into next frame, scale definition, etc.). Several advanced functions were implemented in the software, for example: automatic adaptation of the shape of labeled cells in next frames, possibility to show different versions of the same image (processed images), export images with labeled cells, contrast enhancement for precise labeling. The software can be used for semi-automatic labeling of any kind of objects (including sub-objects) in the image series.

Input Data

The software operates with series of images in defined input directory.


Information about labeled objects: borders, size, color. Images with labeled objects.


Download and run ExpertomicaCellMarker.exe and follow the instructions. The software will be installed into selected directory.

The installation contains:
ExpertomicaCellMarker.exe – the software
dotNetFx35setup.exe - .Net Framework 3.5
vcredist_x86.exe - Visual C++ 2005 Redistributable Package
Help-ExpertomicaCellMarker.pdf – help
several avi files - video presentation of the functionality
Testing data - folder with testing data


Operation system: Windows XP, Vista (32 bit) and 7 (32 bit), Vista (64 bit – compatibility mode XP) and 7 (64 bit – compatibility mode XP)

- .Net Framework 3.5 or higher (included in installation)
- Visual C++ 2005 Redistributable Package (included in installation)


There are several images for testing purposes in install folder in testing data. You can test the software on these datasets to test the functionality. The data are used in the video guides.

Testing data – jpg images of Scenedesmus
Testing data\Entropy RGB-RGB-1,0 – jpg images of processed original images (the images are processed by Expertomica EntropyCalculator)


Expertomica Cell Marker - Software (85.0 MB)

Mirror #1 -


Císař, Štys