Note: A three-dimensional calibration device for the confocal microscope

3D test sample for the calibration and quality control of stimulated emission depletion (STED) and confocal microscopes

Multiple samples are required to monitor and optimize the quality and reliability of quantitative measurements of stimulated emission depletion (STED) and confocal microscopes. Here, we present a single sample to calibrate these microscopes, align their laser beams and measure their point spread function (PSF) in 3D. The sample is composed of a refractive index matched colloidal crystal of silica beads with fluorescent and gold cores. The microscopes can be calibrated in three dimensions using the periodicity of the crystal; the alignment of the laser beams can be checked using the reflection of the gold cores; and the PSF can be measured at multiple positions and depths using the fluorescent cores. It is demonstrated how this sample can be used to visualize and improve the quality of STED and confocal microscopy images. The sample is adjustable to meet the requirements of different NA objectives and microscopy techniques and additionally can be used to evaluate refractive index mismatches as a function of depth quantitatively.

Characterization and Correction of the Geometric Errors in Using Confocal Microscope for Extended Topography Measurement. Part I: Models, Algorithms Development and Validation

This work presents a method for characterizing and correcting the geometric errors of the movement of the lateral stage of Imaging Confocal Microscope (CM) in extended topography measurement. For an extended topography measurement, a defined number of 2D images are taken and stitched by correlation methods. Inaccuracies due to linear displacement, vertical and horizontal straightness errors, angular errors, and squareness errors based on the assumption of the rigid body kinematics are described. A mathematical model for the scale calibration of the X- and Y- coordinates is derived according to the system kinematics, the axis chain vector of CM, and the geometric error functions and their approximations by Legendre polynomials. The correction coefficients of the kinematic modelling are determined by the measured and certified data of a dot grid target standard artefact. To process the measurement data, algorithms for data partitions, fittings of cylinder centers, and determinations of coefficients are developed and validated. During which methods such as form removal, K-means clustering, linear and non-linear Least Squares are implemented. Results of the correction coefficients are presented in Part II based on the experimental studies. The mean residual reduces 29.6% after the correction of the lateral stage errors.

Procedure for Calibrating the Z-axis of a Confocal Microscope: Application for the Evaluation of Structured Surfaces

This work describes a method for the metrological characterization of structured surfaces using a confocal microscope. The proposed method is based on the calculation of texture parameters established in ISO 25178-2:2012. To ensure the traceability of these parameters, a procedure for the calibration of the Z-axis of the confocal microscope is proposed. The calculation of uncertainty associated with each parameter employs the Monte Carlo method, as well as the concept of a virtual instrument. The validity of the algorithms has been verified through the use of synthetic data provided by the National Institute of Standards and Technology (NIST) and physical standards, with minimum differences being obtained between the certified values and calculated or measured values. Finally, using the proposed method, the topography of a structured surface manufactured by laser machining is evaluated, obtaining the most used roughness parameters, as well as their measurement uncertainties and possible correlations. In general, it can be affirmed that it is possible to obtain metrologically reliable results with the proposed method.

Survey statistics of automated segmentations applied to optical imaging of mammalian cells

BACKGROUND

The goal of this survey paper is to overview cellular measurements using optical microscopy imaging followed by automated image segmentation. The cellular measurements of primary interest are taken from mammalian cells and their components. They are denoted as two- or three-dimensional (2D or 3D) image objects of biological interest. In our applications, such cellular measurements are important for understanding cell phenomena, such as cell counts, cell-scaffold interactions, cell colony growth rates, or cell pluripotency stability, as well as for establishing quality metrics for stem cell therapies. In this context, this survey paper is focused on automated segmentation as a software-based measurement leading to quantitative cellular measurements.

METHODS

We define the scope of this survey and a classification schema first. Next, all found and manually filteredpublications are classified according to the main categories: (1) objects of interests (or objects to be segmented), (2) imaging modalities, (3) digital data axes, (4) segmentation algorithms, (5) segmentation evaluations, (6) computational hardware platforms used for segmentation acceleration, and (7) object (cellular) measurements. Finally, all classified papers are converted programmatically into a set of hyperlinked web pages with occurrence and co-occurrence statistics of assigned categories.

RESULTS

The survey paper presents to a reader: (a) the state-of-the-art overview of published papers about automated segmentation applied to optical microscopy imaging of mammalian cells, (b) a classification of segmentation aspects in the context of cell optical imaging, (c) histogram and co-occurrence summary statistics about cellular measurements, segmentations, segmented objects, segmentation evaluations, and the use of computational platforms for accelerating segmentation execution, and (d) open research problems to pursue.

CONCLUSIONS

The novel contributions of this survey paper are: (1) a new type of classification of cellular measurements and automated segmentation, (2) statistics about the published literature, and (3) a web hyperlinked interface to classification statistics of the surveyed papers at https://isg.nist.gov/deepzoomweb/resources/survey/index.html.

Methods to calibrate and scale axial distances in confocal microscopy as a function of refractive index

Accurate distance measurement in 3D confocal microscopy is important for quantitative analysis, volume visualization and image restoration. However, axial distances can be distorted by both the point spread function (PSF) and by a refractive-index mismatch between the sample and immersion liquid, which are difficult to separate. Additionally, accurate calibration of the axial distances in confocal microscopy remains cumbersome, although several high-end methods exist. In this paper we present two methods to calibrate axial distances in 3D confocal microscopy that are both accurate and easily implemented. With these methods, we measured axial scaling factors as a function of refractive-index mismatch for high-aperture confocal microscopy imaging. We found that our scaling factors are almost completely linearly dependent on refractive index and that they were in good agreement with theoretical predictions that take the full vectorial properties of light into account. There was however a strong deviation with the theoretical predictions using (high-angle) geometrical optics, which predict much lower scaling factors. As an illustration, we measured the PSF of a correctly calibrated point-scanning confocal microscope and showed that a nearly index-matched, micron-sized spherical object is still significantly elongated due to this PSF, which signifies that care has to be taken when determining axial calibration or axial scaling using such particles.

Local shear transformations in deformed and quiescent hard-sphere colloidal glasses

We perform a series of deformation experiments on a monodisperse, hard-sphere colloidal glass while simultaneously following the three-dimensional trajectories of roughly 50,000 individual particles with a confocal microscope. In each experiment, we deform the glass in pure shear at a constant strain rate [(1-5)×10(-5) s(-1)] to maximum macroscopic strains (5%-10%) and then reverse the deformation at the same rate to return to zero macroscopic strain. We also measure three-dimensional particle trajectories in an identically prepared quiescent glass in which the macroscopic strain is always zero. We find that shear transformation zones exist and are active in both sheared and quiescent colloidal glasses, revealed by a distinctive fourfold signature in spatial autocorrelations of the local shear strain. With increasing shear, the population of local shear transformations develops more quickly than in a quiescent glass and many of these transformations are irreversible. When the macroscopic strain is reversed, we observe partial elastic recovery, followed by plastic deformation of the opposite sign, required to compensate for the irreversibly transformed regions. The average diameter of the shear transformation zones in both strained and quiescent glasses is slightly more than two particle diameters.

Three-dimensional fibroblast morphology on compliant substrates of controlled negative curvature

Traditionally, cell biological investigations have mostly employed cells growing on flat, two-dimensional, hard substrates, which are of questionable utility in mimicking microenvironments in vivo. We engineered a novel scaffold to achieve cell culture in the third dimension (3D), where fibroblasts lose the strong dorsal-ventral asymmetry in the distribution of cytoskeletal and adhesion components that is induced by growth on flat substrates. The design principle of our new 3D substrate was inspired by recent advances in engineering cellular microenvironments in which rigidity and the patterning of adhesion ligands were tuned on two-dimensional substrates; the engineered substrates enable independent control over biochemical and mechanical factors to elucidate how mechanical cues affect cellular behaviours. The 3D substrates consisted of polyacrylamide scaffolds of highly ordered, uniform pores coated with extracellular matrix proteins. We characterized important parameters for fabrication and the mechanical properties of polyacrylamide scaffolds. We then grew individual fibroblasts in the identical pores of the polyacrylamide scaffolds, examining cellular morphological, actin cytoskeletal, and adhesion properties. We found that fibroblasts sense the local rigidity of the scaffold, and exhibit a 3D distribution of actin cytoskeleton and adhesions that became more pronounced as the pore size was reduced. In small pores, we observed that elongated adhesions can exist without attachment to any solid support. Taken together, our results show that the use of negatively curved surfaces is a simple method to induce cell adhesions in 3D, opening up new degrees of freedom to explore cellular behaviours.