Microscope calibration using laser written fluorescence

Development of hydrogel-based standards and phantoms for non-linear imaging at depth

Significance

Rapid advances in medical imaging technology, particularly the development of optical systems with non-linear imaging modalities, are boosting deep tissue imaging. The development of reliable standards and phantoms is critical for validation and optimization of these cutting-edge imaging techniques.

Aim

We aim to design and fabricate flexible, multi-layered hydrogel-based optical standards and evaluate advanced optical imaging techniques at depth.

Approach

Standards were made using a robust double-network hydrogel matrix consisting of agarose and polyacrylamide. The materials generated ranged from single layers to more complex constructs consisting of up to seven layers, with modality-specific markers embedded between the layers.

Results

These standards proved useful in the determination of the axial scaling factor for light microscopy and allowed for depth evaluation for different imaging modalities (conventional one-photon excitation fluorescence imaging, two-photon excitation fluorescence imaging, second harmonic generation imaging, and coherent anti-Stokes Raman scattering) achieving actual depths of 1550, 1550, 1240, and 1240    μ m , respectively. Once fabricated, the phantoms were found to be stable for many months.

Conclusions

The ability to image at depth, the phantom's robustness and flexible layered structure, and the ready incorporation of "optical markers" make these ideal depth standards for the validation of a variety of imaging modalities.

Fully automated point spread function analysis using PyCalibrate

Reproducibility is severely limited if instrument performance is assumed rather than measured. Within optical microscopy, instrument performance is typically measured using sub-resolution fluorescent beads. However, the process is performed infrequently as it is requires time and suitably trained staff to acquire and then process the bead images. Analysis software still requires the manual entry of imaging parameters. Human error from repeatedly typing these parameters can significantly affect the outcome of the analysis, rendering the results less reproducible. To avoid this issue, PyCalibrate has been developed to fully automate the analysis of bead images. PyCalibrate can be accessed either by executing the Python code locally or via a user-friendly web portal to further improve accessibility when moving between locations and machines. PyCalibrate interfaces with the BioFormats library to make it compatible with a wide range of proprietary image formats. In this study, PyCalibrate analysis performance is directly compared with alternative free-access analysis software PSFj, MetroloJ QC and DayBook 3 and is demonstrated to have equivalent performance but without the need for user supervision.

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, 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 µm 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 the following: 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 are 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 scientific rigor and reproducibility.

Extending resolution within a single imaging frame

The resolution of fluorescence microscopy images is limited by the physical properties of light. In the last decade, numerous super-resolution microscopy (SRM) approaches have been proposed to deal with such hindrance. Here we present Mean-Shift Super Resolution (MSSR), a new SRM algorithm based on the Mean Shift theory, which extends spatial resolution of single fluorescence images beyond the diffraction limit of light. MSSR works on low and high fluorophore densities, is not limited by the architecture of the optical setup and is applicable to single images as well as temporal series. The theoretical limit of spatial resolution, based on optimized real-world imaging conditions and analysis of temporal image stacks, has been measured to be 40 nm. Furthermore, MSSR has denoising capabilities that outperform other SRM approaches. Along with its wide accessibility, MSSR is a powerful, flexible, and generic tool for multidimensional and live cell imaging applications.

Intracellular dynamics of the Sigma-1 receptor observed with super-resolution imaging microscopy

Sigma-1 receptor (Sig1R) is an endoplasmic reticulum (ER)-related membrane protein, that forms heteromers with other cellular proteins. As the mechanism of action of this chaperone protein remains unclear, the aim of the present study was to detect and analyze the intracellular dynamics of Sig1R in live cells using super-resolution imaging microscopy. For that, the Sig1R-yellow fluorescent protein conjugate (Sig1R-YFP) together with fluorescent markers of cell organelles were transfected into human ovarian adenocarcinoma (SK-OV-3) cells with BacMam technology. Sig1R-YFP was found to be located mainly in the nuclear envelope and in both tubular and vesicular structures of the ER but was not detected in the plasma membrane, even after activation of Sig1R with agonists. The super-resolution radial fluctuations approach (SRRF) performed with a highly inclined and laminated optical sheet (HILO) fluorescence microscope indicated substantial overlap of Sig1R-YFP spots with KDEL-mRFP, slight overlap with pmKate2-mito and no overlap with the markers of endosomes, peroxisomes, lysosomes, or caveolae. Activation of Sig1R with (+)-pentazocine caused a time-dependent decrease in the overlap between Sig1R-YFP and KDEL-mRFP, indicating that the activation of Sig1R decreases its colocalization with the marker of vesicular ER and does not cause comprehensive translocations of Sig1R in cells.

Superresolution Linear Optical Imaging in the Far Field

The resolution of optical imaging devices is ultimately limited by the diffraction of light. To circumvent this limit, modern superresolution microscopy techniques employ active interaction with the object by exploiting its optical nonlinearities, nonclassical properties of the illumination beam, or near field probing. Thus, they are not applicable whenever such interaction is not possible, for example, in astronomy or noninvasive biological imaging. Far field, linear optical superresolution techniques based on passive analysis of light coming from the object would cover these gaps. In this Letter, we present the first proof-of-principle demonstration of such a technique for 2D imaging. It works by accessing information about spatial correlations of the image optical field and, hence, about the object itself via measuring projections onto Hermite-Gaussian transverse spatial modes. With a basis of 21 spatial modes in both transverse dimensions, we perform two-dimensional imaging with twofold resolution enhancement beyond the diffraction limit.

Fluorescent nanodiamonds for characterization of nonlinear microscopy systems

Characterizing the performance of fluorescence microscopy and nonlinear imaging systems is an essential step required for imaging system optimization and quality control during longitudinal experiments. Emerging multimodal nonlinear imaging techniques require a new generation of microscopy calibration targets that are not susceptible to bleaching and can provide a contrast across the multiple modalities. Here, we present a nanodiamond-based calibration target for microscopy, designed for facilitating reproducible measurements at the object plane. The target is designed to support day-to-day instrumentation development efforts in microscopy laboratories. The images of a phantom contain information about the imaging performance of a microscopy system across multiple spectral windows and modalities. Since fluorescent nanodiamonds are not prone to bleaching, the proposed imaging target can serve as a standard, shelf-stable sample to provide rapid reference measurements for ensuring consistent performance of microscopy systems in microscopy laboratories and imaging facilities.

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.

A simple, inexpensive and multi-scale 3-D fluorescent test sample for optical sectioning microscopies

Fluorescence standards allow for quality control and for the comparison of data sets across instruments and laboratories in applications of quantitative fluorescence. For example, users of microscopy core facilities can expect a homogenous and time-invariant illumination and an uniform detection sensitivity, which are prerequisites for imaging analysis, tracking or fluorimetric pH or Ca²⁺ -concentration measurements. Similarly, confirming the three-dimensional (3-D) resolution of optical sectioning microscopes calls for a regular calibration with a standardized point source. The test samples required for such measurements are typically different ones, they are often expensive and they depend much on the very microscope technique used. Similarly, the ever-increasing choice among microscope techniques and geometries increases the demand for comparison across instruments. Here, we advocate and demonstrate the multiple uses of a surprisingly versatile and simple 3-D test sample that can complement existing and much more expensive calibration samples: commercial tissue paper labeled with a fluorescent highlighter pen. We provide relevant sample characteristics and show examples ranging from the sub-μm to cm scale, acquired on epifluorescence, confocal, image scanning, two-photon (2P) and light-sheet microscopes.

Microscope calibration protocol for single-molecule microscopy

Single-molecule microscopy allows for the investigation of the dynamics of individual molecules and the visualization of subcellular structures at high spatial resolution. For single-molecule imaging experiments, and particularly those that entail the acquisition of multicolor data, calibration of the microscope and its optical components therefore needs to be carried out at a high level of accuracy. We propose here a method for calibrating a microscope at the nanometer scale, in the sense of determining optical aberrations as revealed by point source localization errors on the order of nanometers. The method is based on the imaging of a standard sample to detect and evaluate the amount of geometric aberration introduced in the optical light path. To provide support for multicolor imaging, it also includes procedures for evaluating the geometric aberration caused by a dichroic filter and the axial chromatic aberration introduced by an objective lens.

Miniaturized integrating sphere light sources based on LEDs for radiance responsivity calibration of optical imaging microscopes

LED-based integrating sphere light sources (LED-ISLSs) in the size of typical microscope slides were developed to calibrate the radiance responsivity of optical imaging microscopes. Each LED-ISLS consists of a miniaturized integrating sphere with a diameter of 4 mm, an LED chip integrated on a printed circuit board, and a thin circular aperture with a diameter of 1 mm as the exit port. The non-uniformity of the radiant exitance of the LED-ISLSs was evaluated to be 0.8%. The normal radiance of the LED-ISLSs in the range of (5∼69) W m^-2 sr^-1 was measured with a standard uncertainty of 1.3% using two precision apertures and a standard silicon photodetector whose spectral responsivity is traceable to an absolute cryogenic radiometer. The LED-ISLSs were applied to calibrate the radiance responsivity of a home-built optical imaging microscope with a standard uncertainty of 2.6∼2.9%. The LED-ISLSs offer a practical way to calibrate the radiance responsivity of various optical imaging microscopes for results comparison and information exchange.

Spinning disk-remote focusing microscopy

Fast confocal imaging was achieved by combining remote focusing with differential spinning disk optical sectioning to rapidly acquire images of live samples at cellular resolution. Axial and lateral full width half maxima less than 5 µm and 490 nm respectively are demonstrated over 130 µm axial range with a 256 × 128 µm field of view. A water-index calibration slide was used to achieve an alignment that minimises image volume distortion. Application to live biological samples was demonstrated by acquiring image volumes over a 24 µm axial range at 1 volume/s, allowing for the detection of calcium-based neuronal activity in Platynereis dumerilii larvae.

Multi-plane remote refocusing epifluorescence microscopy to image dynamic Ca 2 + events

Rapid imaging of multiple focal planes without sample movement may be achieved through remote refocusing, where imaging is carried out in a plane conjugate to the sample plane. The technique is ideally suited to studying the endothelial and smooth muscle cell layers of blood vessels. These are intrinsically linked through rapid communication and must be separately imaged at a sufficiently high frame rate in order to understand this biologically crucial interaction. We have designed and implemented an epifluoresence-based remote refocussing imaging system that can image each layer at up to 20fps using different dyes and excitation light for each layer, without the requirement for optically sectioning microscopy. A novel triggering system is used to activate the appropriate laser and image acquisition at each plane of interest. Using this method, we are able to achieve axial plane separations down to 15  μ m, with a mean lateral stability of ≤ 0.32  μ m displacement using a 60x, 1.4NA imaging objective and a 60x, 0.7NA reimaging objective. The system allows us to image and quantify endothelial cell activity and smooth muscle cell activity at a high framerate with excellent lateral and good axial resolution without requiring complex beam scanning confocal microscopes, delivering a cost effective solution for imaging two planes rapidly. We have successfully imaged and analysed Ca 2 + activity of the endothelial cell layer independently of the smooth muscle layer for several minutes.

Calibration of a phase-only spatial light modulator for both phase and retardance modulation

Liquid crystal spatial light modulators (SLMs) are usually configured and calibrated for phase modulation. However, as they are variable retarders, they also have application as polarization modulators. We show that conventional phase-only calibrations are insufficient for this purpose, and a separate retardance calibration is needed. To overcome this shortcoming we report a simple Twyman-Green interferometer-based setup to realize SLM phase and retardance calibration. For phase calibration, we identify the non-linear, spatially variant response to the drive voltage of the SLM using fringe analysis and both horizontally and vertically polarized incident light. For retardance calibration, we use incident light polarized at 45° and assess the intensity variation. The methods presented are compatible with in situ calibration of SLMs.

3D super-resolution microscopy performance and quantitative analysis assessment using DNA-PAINT and DNA origami test samples

Assessment of the imaging quality in localisation-based super-resolution techniques relies on an accurate characterisation of the imaging setup and analysis procedures. Test samples can provide regular feedback on system performance and facilitate the implementation of new methods. While multiple test samples for regular, 2D imaging are available, they are not common for more specialised imaging modes. Here, we analyse robust test samples for 3D and quantitative super-resolution imaging, which are straightforward to use, are time- and cost-effective and do not require experience beyond basic laboratory and imaging skills. We present two options for assessment of 3D imaging quality, the use of microspheres functionalised for DNA-PAINT and a commercial DNA origami sample. A method to establish and assess a qPAINT workflow for quantitative imaging is demonstrated with a second, commercially available DNA origami sample.

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.