Statistical analysis of 3D localisation microscopy images for quantification of membrane protein distributions in a platelet clot model

Sandra Mayr; Fabian Hauser; Sujitha Puthukodan; Markus Axmann; Janett Göhring; Jaroslaw Jacak

doi:10.1371/journal.pcbi.1007902

Statistical analysis of 3D localisation microscopy images for quantification of membrane protein distributions in a platelet clot model

PLoS Comput Biol. 2020 Jun 30;16(6):e1007902. doi: 10.1371/journal.pcbi.1007902. eCollection 2020 Jun.

Authors

Sandra Mayr¹, Fabian Hauser¹, Sujitha Puthukodan², Markus Axmann¹, Janett Göhring³, Jaroslaw Jacak¹

Affiliations

¹ University of Applied Sciences Upper Austria, Linz, Austria.
² Johannes Kepler University Linz, Linz, Austria.
³ Center for Pathophysiology, Infectiology and Immunology, Institute for Hygiene and Applied Immunology, Medical University of Vienna, Vienna, Austria.

Abstract

We present the software platform 2CALM that allows for a comparative analysis of 3D localisation microscopy data representing protein distributions in two biological samples. The in-depth statistical analysis reveals differences between samples at the nanoscopic level using parameters such as cluster-density and -curvature. An automatic classification system combines multiplex and multi-level statistical approaches into one comprehensive parameter for similarity testing of the compared samples. We demonstrated the biological importance of 2CALM, comparing the protein distributions of CD41 and CD62p on activated platelets in a 3D artificial clot. Additionally, using 2CALM, we quantified the impact of the inflammatory cytokine interleukin-1β on platelet activation in clots. The platform is applicable to any other cell type and biological system and can provide new insights into biological and medical applications.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Blood Platelets / metabolism*
Humans
Machine Learning
Membrane Proteins / metabolism*
Microscopy / methods*
Models, Biological*
P-Selectin / metabolism
Proof of Concept Study
Thrombosis / metabolism*

Substances

Membrane Proteins
P-Selectin
SELP protein, human

Grants and funding

This work was supported by the Interreg Project ATCZ14 Czech-Austrian Center for Supracellular Medical Research (CAC-SuMeR), the Fonds zur Förderung der Wissenschaftlichen Forschung (FWF) (Grant number: W 1250, Funder Id: http://dx.doi.org/10.13039/501100002428), under the Doctorate College program “Nano-Analytics of Cellular Systems(NanoCell)” and stad-Alone Projct '' 3D Lithographical Scaffolds for Stem Cell Differentiation (LiSSCeD) '' Grant number: P 31827. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.