Project „Pattern“ – an online tool for spatial analysis of immunolabeling in electron microscopy

0555850 - ÚMG 2022 RIV CZ eng O - Others
Pinkas, Dominik - Vlčák, Erik - Filimonenko, Vlada - Janáček, J. - Hozák, Pavel
Project „Pattern“ – an online tool for spatial analysis of immunolabeling in electron microscopy.
2021
R&D Projects: GA MŠMT(CZ) LM2018129; GA MŠMT(CZ) EF16_013/0001775; GA MŠMT(CZ) EF18_046/0016045; GA TA ČR(CZ) TE01020118
Research Infrastructure: Czech-BioImaging II - 90129
Institutional support: RVO:68378050
Keywords : Electron microscopy * imunolabeling * colocalization * clustering
OECD category: Cell biology

Evaluation of immunolabelling in EM often lacks unbiased quantitative approach. We have developed an easy-to-use online tool for semi-automatic multi-stage analysis of immunolabeling on EM images spanning particle detection and classification, mathematical and statistical evaluation and visualization of results. This builds on previous work of Philimonenko et al. [1] and Schofer et al. [2]. The tool detects basic particles (“big” and “small” spheres) automatically and results of detection and identification can be manually reviewed and edited. Spatial relations can be analyzed in 2D and 3D microscopic data and along linear structures such as membranes and filaments. The tool uses pair correlation and pair cross-correlation functions for clustering and colocalization evaluation with results presented both numerically and graphically. Labelled structures are visualized via mapping and their spatial relations to other structures or particles are further evaluated as shown by Philimonenko et al. [3]. Statistical significance of detected patterns is calculated and presented in a comprehensive way without requiring a deep insight into statistical analysis. All results and respective settings can be exported. Particle coordinates can be kept on the server for prolonged periods of time to be reused with new settings or compared to new datasets. Projects can be shared with colleagues. For routine analysis, useful results should be available in just a few clicks. The tool is provided to the broad scientific community in open access mode by the IMG within the Czech-BioImaging research infrastructure. The tool emphasizes convenience and understandability of the interface and provides detailed explanations of all results, steps, values and options. The platform is modular and can be expanded with more capabilities in the future.
Permanent Link: http://hdl.handle.net/11104/0330307