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Project „Pattern“ – an online tool for spatial analysis of immunolabeling in electron microscopy
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SYSNO ASEP 0555850 Druh ASEP O - Ostatní výsledky Zařazení RIV O - Ostatní Název Project „Pattern“ – an online tool for spatial analysis of immunolabeling in electron microscopy Tvůrce(i) Pinkas, Dominik (UMG-J) ORCID
Vlčák, Erik (UMG-J)
Filimonenko, Vlada (UMG-J) RID, ORCID
Janáček, J. (CZ)
Hozák, Pavel (UMG-J) RID, ORCIDRok vydání 2021 Jazyk dok. eng - angličtina Země vyd. CZ - Česká republika Klíč. slova Electron microscopy ; imunolabeling ; colocalization ; clustering Vědní obor RIV EB - Genetika a molekulární biologie Obor OECD Cell biology CEP LM2018129 GA MŠMT - Ministerstvo školství, mládeže a tělovýchovy EF16_013/0001775 GA MŠMT - Ministerstvo školství, mládeže a tělovýchovy EF18_046/0016045 GA MŠMT - Ministerstvo školství, mládeže a tělovýchovy TE01020118 GA TA ČR - Technologická agentura ČR Výzkumná infrastruktura Czech-BioImaging II - 90129 - Ústav molekulární genetiky AV ČR, v. v. i. Institucionální podpora UMG-J - RVO:68378050 Anotace 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. Pracoviště Ústav molekulární genetiky Kontakt Nikol Škňouřilová, nikol.sknourilova@img.cas.cz, Tel.: 241 063 217 Rok sběru 2022
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