A Framework for Evaluating the Performance of SMLM Cluster Analysis Algorithms
D. Nieves, J.A. Pike, F. Levet, J. Griffié, D. Sage, E.A.K. Cohen, J.-B. Sibarita, M. Heilemann, D.M. Owen
Single Molecule Localization Microscopy Symposium (SMLMS'21), Lausanne VD, Swiss Confederation, August 31-September 2, 2021.
Single molecule localisation microscopy (SMLM) generates data in the form of Cartesian coordinates of localised fluorophores. Cluster analysis is an attractive route for extracting biologically meaningful information from such data and has been widely applied. Despite the range of developed cluster analysis algorithms, there exists no consensus framework for the evaluation of their performance. Here, we use a systematic approach based on two metrics, the Adjusted Rand Index (ARI) and Intersection over Union (IoU), to score the success of clustering algorithms in diverse simulated clustering scenarios mimicking experimental data. We demonstrate the framework using three analysis algorithms: DBSCAN, ToMATo and KDE, show how to deduce optimal analysis parameters and how they are affected by fluorophore multiple blinking. We propose that these standard conditions and metrics become the basis for future analysis algorithm development and evaluation.
@INPROCEEDINGS(http://bigwww.epfl.ch/publications/nieves2101.html,
AUTHOR="Nieves, D. and Pike, J.A. and Levet, F. and Griffi{\'{e}}, J.
and Sage, D. and Cohen, E.A.K. and Sibarita, J.-B. and Heilemann, M.
and Owen, D.M.",
TITLE="A Framework for Evaluating the Performance of {SMLM} Cluster
Analysis Algorithms",
BOOKTITLE="Single Molecule Localization Microscopy Symposium
({SMLMS'21})",
YEAR="2021",
editor="",
volume="",
series="",
pages="",
address="Lausanne VD, Swiss Confederation",
month="August 31-September 2,",
organization="",
publisher="",
note="")