Quantifying accuracy and heterogeneity in single-molecule super-resolution microscopy

Hesam Mazidi,Tianben Ding,Matthew D. Lew,Arye Nehorai

doi:10.1038/s41467-020-20056-9

Abstract

The resolution and accuracy of single-molecule localization microscopes (SMLMs) are routinely benchmarked using simulated data, calibration rulers, or comparisons to secondary imaging modalities. However, these methods cannot quantify the nanoscale accuracy of an arbitrary SMLM dataset. Here, we show that by computing localization stability under a well-chosen perturbation with accurate knowledge of the imaging system, we can robustly measure the confidence of individual localizations without ground-truth knowledge of the sample. We demonstrate that our method, termed Wasserstein-induced flux (WIF), measures the accuracy of various reconstruction algorithms directly on experimental 2D and 3D data of microtubules and amyloid fibrils. We further show that WIF confidences can be used to evaluate the mismatch between computational models and imaging data, enhance the accuracy and resolution of reconstructed structures, and discover hidden molecular heterogeneities. As a computational methodology, WIF is broadly applicable to any SMLM dataset, imaging system, and localization algorithm.

Highlights

The resolution and accuracy of single-molecule localization microscopes (SMLMs) are routinely benchmarked using simulated data, calibration rulers, or comparisons to secondary imaging modalities
A key question left unresolved by existing Single-molecule localization microscopy (SMLM) methodologies is: How well do the SMLM data, i.e., the images of blinking single molecules (SMs), support the super-resolved image produced by an algorithm? That is, what is our statistical confidence in each localization? Intuitively, one’s interpretation of an SMLM reconstruction could dramatically change by knowing how trustworthy each localization is
In order to estimate the stability of a localization, we measure the degree of photon flux that returns toward the original localization from the perturbed positions (Fig. 1, “Methods”)

Summary

Introduction

The resolution and accuracy of single-molecule localization microscopes (SMLMs) are routinely benchmarked using simulated data, calibration rulers, or comparisons to secondary imaging modalities. Existing metrics for assessing SMLM image quality can be categorized broadly into two classes: those that require knowledge of the ground-truth positions of fluorophores (e.g., Jaccard index and imaging DNA calibration rulers)[6,7,8,9], and those that operate directly on SMLM reconstructions alone, possibly incorporating information from other measurements (e.g., diffraction-limited imaging)[10,11,12] While these methods are able to provide summary or aggregate measures of performance, none of them directly measure the accuracy of individual localizations in an arbitrary SMLM dataset. Such knowledge is critical for harnessing fully the power of SMLM for scientific discovery

Objectives

Results

Conclusion