CytoPacq – On-line Framework for Simulating Fluorescence Microscopy Images

SVOBODA, David and Michal KOZUBEK. CytoPacq – On-line Framework for Simulating Fluorescence Microscopy Images. In Hands-on Image Processing, Robotiker-Tecnalia, Bilbao, Spain. 2009.

Basic information

• Original name: CytoPacq – On-line Framework for Simulating Fluorescence Microscopy Images
• Authors: SVOBODA, David (203 Czech Republic, guarantor, belonging to the institution) and Michal KOZUBEK (203 Czech Republic, belonging to the institution).
• Edition: Hands-on Image Processing, Robotiker-Tecnalia, Bilbao, Spain, 2009.

Other information

• Original language: English
• Type of outcome: Requested lectures
• Field of Study: 20200 2.2 Electrical engineering, Electronic engineering, Information engineering
• Country of publisher: Spain
• Confidentiality degree: is not subject to a state or trade secret
• Organization unit: Faculty of Informatics
• Keywords in English: simulation; biomedical imaging; fluorescence microscopy; cell nucleus
• Tags: International impact

Abstract

In recent years, the biomedicine, like the other fields of research, has become more and more tied up with the computer science. The vast majority of measurements is acquired, stored and further evaluated using the instruments controlled by the appropriate computer hardware and software. In optical microscopy such an equipment has already become a standard. The whole process of observation can be typically split into four principal parts: 1. Specimen preparation, 2. Image transmission, 3. Image acquisition, 4. Image analysis. In the last step of this process a large variety of image processing methods is used. It is clear that the quality and correctness of results of such methods influence the final evaluation and conclusions. That is why each user has to verify whether the selected method is appropriate and whether it performs correctly. For this purpose, we implemented a simulation toolbox called CytoPacq (http://cbia.fi.muni.cz/simulator/) that is capable of simulating the first three steps: * 3D-CytoGen ... generates the digital phantom (specimen preparation) * 3D-OptiGen ... imitates the whole optical system (image transmission) * 3D-AcquiGen ... simulates the behavior of CCD camera (image acquisition) As a result, CytoPacq generates selected synthetic image data as they would look like if acquired by real microscope and camera. Furthermore, the ideal image of an unaffected specimen is also generated. Hence, the synthetic data can be submitted to any image analysis method and the results of such method can be simply compared to the ideal image and the quality can be evaluated. Currently, three types of objects can be generated (microspheres, nuclei of HL-60 cells, and nuclei of granulocytes). The generation of new types of phantoms (e.g. tissue clusters) is currently under development.

Links

• LC535, research and development project: Name: Dynamika a organizace chromosomů během buněčného cyklu v normě a patologii

Investor: Ministry of Education, Youth and Sports of the CR, Dynamika a organizace chromosomů během buněčného cyklu v normě a patologii

• 2B06052, research and development project: Name: Vytipování markerů, screening a časná diagnostika nádorových onemocnění pomocí vysoce automatizovaného zpracování multidimenzionálních biomedicínských obrazů (Acronym: Biomarker)

Investor: Ministry of Education, Youth and Sports of the CR, Determination of markers, screening and early diagnostics of cancer diseases using highly automated processing of multidimensional biomedical images