Image simulation for biological microscopy: microlith

TL;DR

This paper introduces microlith, an open-source toolbox that accurately simulates 3D images in biological microscopy with partially coherent illumination, aiding in understanding and detecting nanoscale structural changes.

Contribution

The paper presents microlith, a novel simulation tool capable of modeling partially coherent microscopy images, which was previously difficult to achieve.

Findings

Microlith accurately predicts bright-field and dark-field images.

Dark-field microscopy sensitivity to 10nm scale mass distributions.

Proposes a new method for detecting nanoscale changes in axonemes.

Abstract

Image simulation remains under-exploited for the most widely used biological phase microscopy methods, because of difficulties in simulating partially coherent illumination. We describe an open-source toolbox, microlith (https://code.google.com/p/microlith), which accurately predicts three-dimensional images of a thin specimen observed with any partially coherent imaging system, including coherently illuminated and incoherent, self-luminous specimens. Its accuracy is demonstrated by comparing simulated and experimental bright-field and dark-field images of well-characterized amplitude and phase targets, respectively. The comparison provides new insights about the sensitivity of the dark-field microscope to mass distributions in isolated or periodic specimens at the length-scale of 10nm. Based on predictions using microlith, we propose a novel approach for detecting nanoscale structural changes in a beating axoneme using a dark-field microscope.