Intensity calibration and flat-field correction for fluorescence microscopes

Hyperspectral Detection of the Fluorescence Shift between Chirality-Sorted Empty and Water-Filled Single-Wall Carbon Nanotube Enantiomers

Single-wall carbon nanotubes (SWCNTs) have extraordinary electronic and optical properties that depend strongly on their exact chiral structure and their interaction with their inner and outer environment. The fluorescence (PL) of semiconducting SWCNTs, for instance, will shift depending on the molecules with which the SWCNT's hollow core is filled. These interaction-induced shifts are challenging to resolve on the ensemble level in samples containing a mixture of different filling contents due to the relatively large inhomogeneous line width of the ensemble SWCNT PL compared to the size of these shifts. To circumvent this inhomogeneous broadening, single-tube spectroscopy and hyperspectral imaging are often applied, which until now required time-consuming statistical studies. Here, we present hyperspectral PL microscopy combined with automated SWCNT segmenting based on either principal component analysis or a convolutional neural network, capable of both spatially and spectrally resolving the PL along the length of many individual SWCNTs at the same time and automatically fitting peak positions and line widths of individual SWCNTs. The methodology is demonstrated by accurately determining the emission shifts and line widths of thousands of left- and right-handed empty and water-filled SWCNTs coated with a chiral surfactant, resulting in four statistical distributions which cannot be resolved in ensemble spectroscopy of unsorted samples. The results demonstrate a robust method to quickly probe ensemble properties with single-enantiomer spectral resolution. Moreover, it promises to be an absolute quantitative method to characterize the relative abundances of SWCNTs with different handedness or filling content in macroscopic samples, simply by counting individual species.

Short tandem repeats bind transcription factors to tune eukaryotic gene expression

Short tandem repeats (STRs) are enriched in eukaryotic cis-regulatory elements and alter gene expression, yet how they regulate transcription remains unknown. We found that STRs modulate transcription factor (TF)-DNA affinities and apparent on-rates by about 70-fold by directly binding TF DNA-binding domains, with energetic impacts exceeding many consensus motif mutations. STRs maximize the number of weakly preferred microstates near target sites, thereby increasing TF density, with impacts well predicted by statistical mechanics. Confirming that STRs also affect TF binding in cells, neural networks trained only on in vivo occupancies predicted effects identical to those observed in vitro. Approximately 90% of TFs preferentially bound STRs that need not resemble known motifs, providing a cis-regulatory mechanism to target TFs to genomic sites.

Laminar flow-based microfluidic systems for molecular interaction analysis-Part 2: Data extraction, processing and analysis

The rate at which fluorescently-labeled biomolecules, that are flowing at a constant speed in a microfluidic channel, diffuse into an adjacent buffer stream can be used to calculate the diffusion coefficient of the molecule, which then gives a measure of its size. Experimentally, determining the rate of diffusion involves capturing concentration gradients in fluorescence microscopy images at different distances along the length of the microfluidic channel, where distance corresponds to residence time, based on the flow velocity. The preceding chapter in this journal covered the development of the experimental setup, including information about the microscope camera detection systems used to acquire fluorescence microscopy data. In order to calculate diffusion coefficients from fluorescence microscopy images, intensity data are extracted from the images and then appropriate methods of processing and analyzing the data, including the mathematical models used for fitting, are applied to the extracted data. This chapter begins with a brief overview of digital imaging and analysis principles, before introducing custom software for extracting the intensity data from the fluorescence microscopy images. Subsequently, methods and explanations for performing the necessary corrections and appropriate scaling of the data are provided. Finally, the mathematics of one-dimensional molecular diffusion is described, and analytical approaches to obtaining the diffusion coefficient from the fluorescence intensity profiles are discussed and compared.

Quality assessment in light microscopy for routine use through simple tools and robust metrics

Although there is a need to demonstrate reproducibility in light microscopy acquisitions, the lack of standardized guidelines monitoring microscope health status over time has so far impaired the widespread use of quality control (QC) measurements. As scientists from 10 imaging core facilities who encounter various types of projects, we provide affordable hardware and open source software tools, rigorous protocols, and define reference values to assess QC metrics for the most common fluorescence light microscopy modalities. Seven protocols specify metrics on the microscope resolution, field illumination flatness, chromatic aberrations, illumination power stability, stage drift, positioning repeatability, and spatial-temporal noise of camera sensors. We designed the MetroloJ_QC ImageJ/Fiji Java plugin to incorporate the metrics and automate analysis. Measurements allow us to propose an extensive characterization of the QC procedures that can be used by any seasoned microscope user, from research biologists with a specialized interest in fluorescence light microscopy through to core facility staff, to ensure reproducible and quantifiable microscopy results.

Single Image-Based Vignetting Correction for Improving the Consistency of Neural Activity Analysis in 2-Photon Functional Microscopy

High-resolution functional 2-photon microscopy of neural activity is a cornerstone technique in current neuroscience, enabling, for instance, the image-based analysis of relations of the organization of local neuron populations and their temporal neural activity patterns. Interpreting local image intensity as a direct quantitative measure of neural activity presumes, however, a consistent within- and across-image relationship between the image intensity and neural activity, which may be subject to interference by illumination artifacts. In particular, the so-called vignetting artifact—the decrease of image intensity toward the edges of an image—is, at the moment, widely neglected in the context of functional microscopy analyses of neural activity, but potentially introduces a substantial center-periphery bias of derived functional measures. In the present report, we propose a straightforward protocol for single image-based vignetting correction. Using immediate-early gene-based 2-photon microscopic neural image data of the mouse brain, we show the necessity of correcting both image brightness and contrast to improve within- and across-image intensity consistency and demonstrate the plausibility of the resulting functional data.

Regression Based Iterative Illumination Compensation Method for Multi-Focal Whole Slide Imaging System

Image quality, resolution and scanning time are critical in digital pathology. In order to create a high-resolution digital image, the scanner systems execute stitching algorithms to the digitized images. Due to the heterogeneity of the tissue sample, complex optical path, non-acceptable sample quality or rapid stage movement, the intensities on pictures can be uneven. The evincible and visible intensity distortions can have negative effect on diagnosis and quantitative analysis. Utilizing the common areas of the neighboring field-of-views, we can estimate compensations to eliminate the inhomogeneities. We implemented and validated five different approaches for compensating output images created with an area scanner system. The proposed methods are based on traditional methods such as adaptive histogram matching, regression-based corrections and state-of-the art methods like the background and shading correction (BaSiC) method. The proposed compensation methods are suitable for both brightfield and fluorescent images, and robust enough against dust, bubbles, and optical aberrations. The proposed methods are able to correct not only the fixed-pattern artefacts but the stochastic uneven illumination along the neighboring or above field-of-views utilizing iterative approaches and multi-focal compensations.

Revealing enzyme functional architecture via high-throughput microfluidic enzyme kinetics

Systematic and extensive investigation of enzymes is needed to understand their extraordinary efficiency and meet current challenges in medicine and engineering. We present HT-MEK (High-Throughput Microfluidic Enzyme Kinetics), a microfluidic platform for high-throughput expression, purification, and characterization of more than 1500 enzyme variants per experiment. For 1036 mutants of the alkaline phosphatase PafA (phosphate-irrepressible alkaline phosphatase of Flavobacterium), we performed more than 670,000 reactions and determined more than 5000 kinetic and physical constants for multiple substrates and inhibitors. We uncovered extensive kinetic partitioning to a misfolded state and isolated catalytic effects, revealing spatially contiguous regions of residues linked to particular aspects of function. Regions included active-site proximal residues but extended to the enzyme surface, providing a map of underlying architecture not possible to derive from existing approaches. HT-MEK has applications that range from understanding molecular mechanisms to medicine, engineering, and design.

Anatase Titanium Dioxide Imparts Photoluminescent Properties to PA2200 Commercial 3D Printing Material to Generate Complex Optical Imaging Phantoms

Selective laser sintering (SLS) is a prominent 3D printing modality that typically uses a polyamide (PA) powder as the substrate. One commercially available SLS material is known as PA2200, which is comprised of nylon 12 and titanium dioxide (TiO₂) and is widely used to generate 3D-printed parts. Here, we report a unique optical photoluminescence (PL) characteristic of native, white PA2200, in which it yields a persistent, phosphorescence-type emission. An analysis of luminescence imaging data with emission measurements demonstrated that the anatase phase of the titanium dioxide additive is the source of the persistent PL properties. This characteristic of PA2200 enables advanced optical imaging applications, as demonstrated by luminescence imaging of an anatomical rat skeleton and a novel Derenzo-type phantom on a commercial image station. In summary, the light emission properties of PA2200 induced by the presence of anatase titanium dioxide open the door to a vast new array of complex optical applications, including the generation of imaging phantoms for training, calibration, and quality control.

Imaging and Analysis of Neurofilament Transport in Excised Mouse Tibial Nerve

Neurofilament protein polymers move along axons in the slow component of axonal transport at average speeds of ~0.35-3.5 mm/day. Until recently the study of this movement in situ was only possible using radioisotopic pulse-labeling, which permits analysis of axonal transport in whole nerves with a temporal resolution of days and a spatial resolution of millimeters. To study neurofilament transport in situ with higher temporal and spatial resolution, we developed a hThy1-paGFP-NFM transgenic mouse that expresses neurofilament protein M tagged with photoactivatable GFP in neurons. Here we describe fluorescence photoactivation pulse-escape and pulse-spread methods to analyze neurofilament transport in single myelinated axons of tibial nerves from these mice ex vivo. Isolated nerve segments are maintained on the microscope stage by perfusion with oxygenated saline and imaged by spinning disk confocal fluorescence microscopy. Violet light is used to activate the fluorescence in a short axonal window. The fluorescence in the activated and flanking regions is analyzed over time, permitting the study of neurofilament transport with temporal and spatial resolution on the order of minutes and microns, respectively. Mathematical modeling can be used to extract kinetic parameters of neurofilament transport including the velocity, directional bias and pausing behavior from the resulting data. The pulse-escape and pulse-spread methods can also be adapted to visualize neurofilament transport in other nerves. With the development of additional transgenic mice, these methods could also be used to image and analyze the axonal transport of other cytoskeletal and cytosolic proteins in axons.

Comparison of cell volume measurements by fluorescence and absorption exclusion microscopy

There are two light microscopic methods for cell volume measurement based on volume exclusion. One method, sometimes referred to as FLEX, utilises negative staining by an external fluorescent dye, and cell volume is found from attenuation of fluorescence under a wide-field microscope. The other method (TTD) is based on exclusion of an external absorbing dye, resulting in an increased intensity of transmission image. In this work, we compared these two methods. TTD measurements were consistent, reproducible and identical to those obtained by confocal scanning. In our hands, FLEX based on either sodium fluorescein of fluorescent dextran, usually resulted in underestimation of cell volume, which were insignificant in shallow chambers but became more severe with increased chamber depth. We have not been able to exactly pinpoint the source of the problem; it may have been undetected accumulation of dye in the cells or, more likely, some unappreciated aspects of image formation under epi-illumination. We also discuss applicability of both methods to in-flow volume measurements. LAY DESCRIPTION: Cell volume is a parameter important for many cell biological and physiological applications, and many different methods have been proposed for its measurement. Two light microscopic methods based on volume exclusion deserve special attention due to their speed and simplicity. In one of them (transmission-through-dye, or TTD), cells are placed in a shallow chamber, and a strongly absorbing external dye is added to the cell-containing medium. The sample is imaged in transmission at a wavelength of maximum dye absorption. Because cells with intact membranes exclude the dye, they appear brighter on a transmission image, and their contrast quantitatively reflects cell thickness. By summation of thickness values over the cell area, cell volume can be obtained. The other method sometimes referred to as FLEX utilises exclusion of a fluorescent dye. Cells appear darker than the background under wide-field fluorescence observation in accordance with their thicknesses, and cell volume is computed by thickness summation over the area, like in TTD. In this work, we compared the accuracy of TTD and FLEX for volume measurements. TTD and confocal scanning produced virtually identical results, which suggests that TTD data are accurate. On the other hand, cell volumes measured by FLEX were consistently smaller than by TTD. The discrepancy always increased with the depth of the chamber, although the exact relationship varied between experiments. By contrast, TTD results were insensitive to chamber depth. Thus, it appears that FLEX underestimates cell volume. The reason for that is not entirely clear. Accumulation of the fluorescent dye inside the cell could be a possibility, although we found no evidence for that. Most likely, the reason lies with some unappreciated aspects of wide-field fluorescence image formation, which has not been well-characterised for the type of negative staining used in FLEX. In our opinion, TTD is the method of choice, at least for stationary cells. On the other hand, due to linear dependence of intensity on volume, FLEX might offer advantages for high-throughput flow volume imaging, although realisation of such an experiment has yet to be worked out.

Size, shape, and flexibility influence nanoparticle transport across brain endothelium under flow

Nanoparticle-based therapeutic formulations are being increasingly explored for the treatment of various ailments. Despite numerous advances, the success of nanoparticle-based technologies in treating brain diseases has been limited. Translational hurdles of nanoparticle therapies are attributed primarily to their limited ability to cross the blood-brain barrier (BBB), which is one of the body's most exclusive barriers. Several efforts have been focused on developing affinity-based agents and using them to increase nanoparticle accumulation at the brain endothelium. Very little is known about the role of fundamental physical parameters of nanoparticles such as size, shape, and flexibility in determining their interactions with and penetration across the BBB. Using a three-dimensional human BBB microfluidic model (μHuB), we investigate the impact of these physical parameters on nanoparticle penetration across the BBB. To gain insights into the dependence of transport on nanoparticle properties, two separate parameters were measured: the number of nanoparticles that fully cross the BBB and the number that remain associated with the endothelium. Association of nanoparticles with the brain endothelium was substantially impacted by their physical characteristics. Hard particles associate more with the endothelium compared to soft particles, as do small particles compared to large particles, and spherical particles compared to rod-shaped particles. Transport across the BBB also exhibited a dependence on nanoparticle properties. A nonmonotonic dependence on size was observed, where 200 nm particles exhibited higher BBB transport compared to 100 and 500 nm spheres. Rod-shaped particles exhibited higher BBB transport when normalized by endothelial association and soft particles exhibited comparable transport to hard particles when normalized by endothelial association. Tuning nanoparticles' physical parameters could potentially enhance their ability to cross the BBB for therapeutic applications.

Q&A: Array tomography

Array tomography encompasses light and electron microscopy modalities that offer unparalleled opportunities to explore three-dimensional cellular architectures in extremely fine structural and molecular detail. Fluorescence array tomography achieves much higher resolution and molecular multiplexing than most other fluorescence microscopy methods, while electron array tomography can capture three-dimensional ultrastructure much more easily and rapidly than traditional serial-section electron microscopy methods. A correlative fluorescence/electron microscopy mode of array tomography furthermore offers a unique capacity to merge the molecular discrimination strengths of multichannel fluorescence microscopy with the ultrastructural imaging strengths of electron microscopy. This essay samples the first decade of array tomography, highlighting applications in neuroscience.

Methods for cell volume measurement

Volume is an essential characteristic of a cell, and this review describes the main methods of its measurement that have been used in the past several decades. The discussed methods include various implementations of light scattering, estimates based on one or two cell dimensions, surface scanning, fluorescence confocal and transmission slice-by-slice imaging, intracellular volume markers, displacement of extracellular solution, quantitative phase imaging, radioactive methods, and some others. Suitability of these methods to some typical samples and applications is discussed. © 2017 International Society for Advancement of Cytometry.

A BaSiC tool for background and shading correction of optical microscopy images

Quantitative analysis of bioimaging data is often skewed by both shading in space and background variation in time. We introduce BaSiC, an image correction method based on low-rank and sparse decomposition which solves both issues. In comparison to existing shading correction tools, BaSiC achieves high-accuracy with significantly fewer input images, works for diverse imaging conditions and is robust against artefacts. Moreover, it can correct temporal drift in time-lapse microscopy data and thus improve continuous single-cell quantification. BaSiC requires no manual parameter setting and is available as a Fiji/ImageJ plugin.

Calibrated brightfield-based imaging for measuring intracellular protein concentration

Intracellular protein concentration is an essential cell characteristic, which manifests itself through the refractive index. The latter can be measured from two or more mutually defocused brightfield images analyzed using the TIE (transport-of-intensity equation). In practice, however, TIE does not always achieve quantitatively accurate results on biological cells. Therefore, we have developed a calibration procedure that involves successive imaging of cells in solutions containing different amounts of added protein. This allows one to directly relate the output of TIE (T) to intracellular protein concentration C (g/L). The resultant relationship has a simple form: C ≈ 1.0(T/V), where V is the cell volume (μm³ ) and 1.0 is an empirical coefficient. We used calibrated TIE imaging to characterize the regulatory volume increase (RVI) in adherent HeLa cells placed in a hyperosmotic solution. We found that while no RVI occurs over the first 30-60 min, the protein concentration fully recovers after 20 h. Because interpretation of such long experiments may depend on whether protein concentration varies significantly throughout the cell cycle, we measured this parameter in three cell lines: HeLa, MDCK and DU145. Our data indicate that protein concentration remains relatively stable in these cells. © 2017 International Society for Advancement of Cytometry.

An automated imaging system for radiation biodosimetry

We describe here an automated imaging system developed at the Center for High Throughput Minimally Invasive Radiation Biodosimetry. The imaging system is built around a fast, sensitive sCMOS camera and rapid switchable LED light source. It features complete automation of all the steps of the imaging process and contains built-in feedback loops to ensure proper operation. The imaging system is intended as a back end to the RABiT-a robotic platform for radiation biodosimetry. It is intended to automate image acquisition and analysis for four biodosimetry assays for which we have developed automated protocols: The Cytokinesis Blocked Micronucleus assay, the γ-H2AX assay, the Dicentric assay (using PNA or FISH probes) and the RABiT-BAND assay.