Laboratory of Confocal and Electron Microscopy



Laboratory team


Head of Laboratory

Tomasz Skrzypek, PhD

Assistant Professor (research)

tel. +48 (81) 454 56 11
ORCID: 0000-0003-1836-3734


Emil Zięba, MSc

Technical and scientific researcher


tel. +48 (81) 454 56 11



      The Laboratory of Confocal and Electron Microscopy conducts research in the field of biological, biomedical and chemical sciences. The main stream of research concerns changes in the small intestines of mammals, particularly those which occur spontaneously within the mucous membrane during the maturation process. Furthermore, it investigates changes induced by nutrient and anti-nutrient factors as well as growth stimulators/inhibitors, and other related factors/processes. Within the scope of biomedical research, the Laboratory undertakes examination of the structure and chemical composition of mammals’ bones and analyses of bone post-fracture unions. The parasitology research aims to identify parasitic species and to document changes in the host tissue caused by parasites in the organs.

The Laboratory cooperates with biological and biomedical science bodies in order to use of light and transmission electron microscopes (TEM) and scanning electron microscopes (SEM) in the joint research. These microscopes enable the researchers to examine the sample, record the analysis in the form of high resolution photomicrographs and study the image.

The research interests include:

  • imaging of the ultrastructure of the body surface of e.g. protozoans, invertebrates and vertebrate animals, as well as plant organs for taxonomic purposes,
  • imaging and analysis of the changes within the ultrastructure of animal and plant organs, caused by chemical and physical factors,
  • imaging and analysis of frozen biological sample with the use of an SEM and a cryo-transfer system without any practical chemistry procedures,
  • X-ray elemental analysis of the selected spots of the sample (with the use of SEM and EDS – energy-dispersive X-ray spectroscopy technique),
  • imaging of the microorganism ultrastructure in a TEM, imaging of the tissue and cell ultrastructure in an SEM,
  • elemental analysis and specific element distribution analysis of the sample composition (with the use of TEM and EELS – electron energy loss spectroscopy technique),
  • imaging and recording of lesions and other changes present in the cell, tissue and organ ultrastructure (particularly in the gastrointestinal tract),
  • imaging of diffraction patterns in the material texture, mapping the orientation of individual grains in polycrystalline material and the identification of the phases of crystallites (with EBSD – electron backscattered diffraction detector in SEM chamber),
  • imaging of surface structures, defects and changes caused by chemical and physical factors (implants, fillings, etc.) and structural changes in biological samples as well as solid and liquid materials.


The ZEISS Ultra Plus Field Emission microscope is a highly advanced SEM used for biological, biomedical, chemical and material analyses. The microscope is equipped with four imaging detectors (two of which allow observation of structural changes), an energy-dispersive X-ray detector (X-ray analysis), an EBSD detector (X-ray diffraction) and a cryo-transfer system which allows observation of the surfaces and boundaries of biological specimens and liquid substances, without the need for their preparation. Additionally, the microscope has a charge compensation system for the imaging of non-conducting samples. The magnifications range from 10 to 1,000,000x, with a resolution of 0.8 nm.

            The medium voltage Zeiss LIBRA 120 TEM is a highly advanced instrument used for biological, biomedical, chemical and material analyses. It is equipped with an energy filter and an EELS system, applied for a chemical analysis and mapping of elemental distribution in the sample. The microscope features a variable voltage of 80 keV and 120 keV, with a maximum magnification of 1,000,000x and resolution of 0.34 nm.

            The ZEISS LSM 700 inverted confocal microscope attached to an inverted Axio Observer Z1 microscope supports transmitted light research methods, epifluorescence and Nomarski contrast (DIC). As it is fully automated, it is used to examine tissues and analyse intracellular processes of live cell cultures, intercellular interactions, microinjections, etc.


Specimen preparation instruments:

  • an automated spin tissue processor for biological specimen processing (Thermo Scientific, STP 120),
  • drying sample preparation systems (Polaron, Critical Point Drier Apparatus 7501),
  • a modular tissue embedding centre (Thermo Scientific Microm EC 350)
  • a slide stainer Microm HMS 740-Thermo Scientific,
  • cutting material (sections) systems: cryostat (ZEISS, HYRAX C25), microtome (Thermo Scientific HM 355S) and RMC Power Tome XL ultramicrotomes,
  • gold/palladium and chrome sputter coater and carbon coating systems (conventional and high-resolution appliances) (Emitech, SC7620 Sputter Coater, CA7025 Carbon Accessory; K575X Emitech),
  • Scanning microscope Cryo system (Polaron)