Optimizing sampling efficiency of histological quantification

• Thesis title in Czech: Vzorkování a optimalizace designu v kvantitativní histologii
• Thesis title in English: Optimizing sampling efficiency of histological quantification
• English key words: photomicrography; quantitative microscopy; stereology; sampling
• Academic year of topic announcement: 2024/2025
• Thesis type: dissertation
• Thesis language: angličtina
• Department: Ústav histologie a embryologie (14-40)
• Supervisor: prof. MUDr. Mgr. Zbyněk Tonar, Ph.D.

Guidelines

The candidate will review the state-of-the-art knowledge on the topic of the thesis. The student will actively master the methods required for research, namely: bright-field, fluorescence and confocal microscopy; scanning of histological slides; processing of tissue blocks in a histological laboratory and production of histological slides including immunohistochemical protocols; microphotography; stereological quantification of numbers, lengths, areas and volumes of microscopic objects using geometric grids; descriptive statistics and statistical hypothesis testing; power sample analysis. The candidate will thoroughly master the microscopic anatomy of human organ systems and major animal models used in biomedicine. The student will master the principles of experimental design in histology. The candidate will become proficient in spoken and written English at a minimum level of B2, preferably C1. The candidate will become proficient in scientific writing, in particular: a review of current knowledge in the field; clear formulation of the research questions and testable hypotheses; reproducible description of methodological procedures; clear presentation and documentation of data; interpretation of their significance; and formulation of conclusions. The candidate will becoma a valid collaborator of the training team and external collaborators. He/she will publish original results of his/her work in internationally recognized journals and present them at national and international conferences. He/she will apply for a research student grant and learn the principles of obtaining, conducting and defending research projects. The candidate will aim to become a fully competent, independent and internationally competitive researcher in the field of quantitative histology.

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References

Gundersen HJ, Osterby R (1981). Optimizing sampling efficiency of stereological studies in biology: or 'do more less well!'. Journal of Microscopy, 121, 65–73. doi: 10.1111/j.1365–2818.1981.tb01199.x.

Gundersen HJG, Vedel Jensen EB, Kieu K, Nielsen J (1999). The efficiency of systematic sampling in stereology reconsidered. Journal of Microscopy, 193, 199–211. doi: 10.1046/j.1365–2818.1999.00457.x

Jiřík M, Bartoš M, Tomášek P, Malečková A, Kural T, Horáková J, Lukáš D, Suchý T, Kochová P, Hubálek Kalbáčová M, Králíčková M, Tonar Z. (2018). Generating standardized image data for testing and calibrating quantification of volumes, surfaces, lengths, and object counts in fibrous and porous materials using X–ray microtomography. Microscopy Research and Techniques, 81, 551–568. doi:10.1002/jemt.23011.

Kolinko Y, Malečková A, Kochová P, Grajciarová M, Blassová T, Kural T, Trailin A, Červenková L, Havránková J, Vištejnová L, Tonarová P, Moulisová V, Jiřík M, Zavaďáková A, Tichánek F, Liška V, Králíčková M, Witter K, Tonar Z (2021). Using virtual microscopy for the development of sampling strategies in quantitative histology and design-based stereology. Anat Histol Embryol. In Press. doi: 10.1111/ahe.12765.

Tschanz S, Schneider JP, Knudsen L (2014). Design–based stereology: Planning, volumetry and sampling are crucial steps for a successful study. Annals of Anatomy 196, 3–11. doi:10.1016/j.aanat.2013.04.011

Preliminary scope of work in English

Only a fraction of specimens under study are usually selected for quantification in histology. Multilevel sampling or tissue probes, slides, and fields of view (FOVs) in the regions of interest (ROIs) are required. In general, all parts of the organs under study should be given the same probability to be taken into account, i.e., the sampling should be unbiased on all levels. The objective of the study will be to provide data on spatial distribution of various tissue components, such as cells, and extracellular matrix, in the context of developing sampling strategies of FOVs for stereological quantification. The outcomes will be formulated as implications for the most common situations, such as exhaustive sampling of ROIs, sampling ROIs of different sizes, sampling the same ROIs for multiple histological methods, sampling more ROIs with variable intensities or using various objectives, multistage sampling, and virtual whole-slide sampling. Recommendations will be given in order to optimize the efficiency of histological quantification to prevent oversampling or undersampling.