Tissue-Like 3D Standard and Protocols for Microscope Quality Management

This article outlines a global study conducted by the Association of Biomedical Resource Facilities (ABRF) Light Microscopy Research Group (LMRG). The results present a novel 3D tissue-like biologically relevant standard sample that is affordable and straightforward to prepare. Detailed sample preparation and instrument specific image acquisition protocols and image analysis methods are presented and made available to the community. The standard consists of sub-resolution and large well characterized relative intensity fluorescence microspheres embedded in a 120 {micro}m thick 3D gel with a refractive index of 1.365. The standard allows the evaluation of several properties as a function of depth. These include: 1) microscope resolution with automated analysis of the point spread function (PSF), 2) automated signal-to-noise- ratio analysis, 3) calibration and correction of fluorescence intensity loss, and 4) quantitative relative intensity. Results demonstrate expected refractive index mismatch dependent losses in intensity and resolution with depth but the relative intensities of different objects at similar depths were maintained. This is a robust standard showing reproducible results across laboratories, microscope manufacturers and objective lens types (e.g. magnification, immersion medium). Thus, these tools will be valuable for the global community to benchmark fluorescence microscopes and will contribute to improved rigor and reproducibility.