1. processing and measurement of 3D image data (development of new methods and SW implementations, applications): image analysis, stereology, spatial statistics, 3D reconstructions
2. first- and second-order stereological methods: studies of method variance, development of new methods and SW, consultations, training
3. 3D microscopy of biological objels: a) confocal and two-photon microscopy: data analysis, applications of recent fluorescence methods and two-photon microscopy methods, calibration measurements, service and maintenance of Leica SP2 AOBS confocal microscope with 2-photon excitation and Leica SPE microscope, consultations, training 2) optical projection tomography in transmition or fluorescent mode, preparation and clearing of samples
4. application of methods for processing and evaluation of image data in studies of biological specimens, e.g. capillaries in human placenta, tooth pulp, rat muscle and brain, internal structure of Noeway spruce needles, in studies of cell components, such as nuclear structures and endoplasmic reticulum
5. administration of the computer network in the Krč area and corresponding services for the Institute of Physiology including administration of www pages, statistical analyses, coordination of the signalization system

Research activities of the Department of Biomathematics are focussed mainly on analysis and measurement of 3-D image data using stereology, 3-D image processing and computer reconstructions. Further, consultancy and extensive technical support on networking, computer graphics, statistics, stereology, and confocal microscopy are provided to the Academy institutes located in the Krč area but mainly to the Institute of Physiology.

In the Krč area, the following technical support is provided:

1. Administration of the local computer network (LAN) (domain: biomed.cas.cz) with approx. 1000 stations (PC) and mailboxes. Administration of servers providing basic services (DNS, DHCP, Mail, Web, Antispam and Antivirus, Firewall, FTP, Backup).

2. Evaluation of the LAN performance and planning its further development, taking into account the ever increasing demands on the LAN performance.

3. Servicing and maintaining two-photon and confocal microscopes.
    

The technical support provided to the Institute of Physiology comprises:

1. Maintenance of the LAN including installation of network supporting software, administration, maintenance and and upgrading information displayed at the Institute webpages and Intranet.

2. Consultations in statistics and statistical analyses of scientific results.

3. Maintenance of the C.A.S.T.- GRID system (Olympus) for stereology, including consultations on stereological methods.
    

Research activities of the Department comprise both the development of new methods and programmes as well as a number of applications in cooperation with other laboratories. New stereological methods are developed and implemented together with other methods for the measurement of volume, surface area, length and other geometrical characteristics of biological objects, such as characteristics of their spatial distribution. The efficiency and applicability of the methods are compared at the theoretical as well as practical level. The design, development and computer implementation of methods for 3-D image analysis and reconstruction of biological objects from their serial sections and interactive visualization of these objects also belong to the priorities. Among the extensive number of the software modules developed, there are more than 80 modules for stereology, image processing and analysis in the ELLIPSE (ViDiTo, SR) environment, 150 modules for image processing running in the IRIS EXPLORER (NAG, UK) programming environment, Rapid 3D software system for 3D visualization of large specimens, STESYS software for generation of stereological test systems, and modules in ImageJ environment. The images of serial sections are captured predominantly by using confocal microscopy. Many applications, concerning above all confocal microscopy and stereology, run in cooperation with laboratories of the Institute of Physiology, other Academy institutes and universities in the Czech Republic and abroad (e.g., Ljubljana in Slovenia, Loma Linda in USA, Genoa in Italy, Thessaloniki in Greece). Let us mention studies of the capillary bed of placental villi, skeletal muscle fibres, brain and tooth pulp tissue, components of chick embryonic kidney, membrane microdomains in mast cells, anatomical structure of needles, etc. Another source of serial slices is represented by medical tomographical imaging systems like CT, MR, SPECT that are located at cooperating institutes in Prague. Exploiting these sources the problem of registration (alignment) of pictures of neighboring slices are solved and modern methods for their registration, volume or surface reconstruction and visualization are developed and implemented. In the framework of the „Fluorescence Microscopy in Biological and Medical Research“ Centre applications of recent advanced fluorescence techniques and two-photon microscopy methods are developed.