BigStitcher: reconstructing high-resolution image datasets of cleared and expanded samples.

Light-sheet imaging of cleared and expanded samples creates terabyte-sized datasets that consist of many unaligned three-dimensional image tiles, which must be reconstructed before analysis. We developed the BigStitcher software to address this challenge. BigStitcher enables interactive visualization, fast and precise alignment, spatially resolved quality estimation, real-time fusion and deconvolution of dual-illumination, multitile, multiview datasets.

A practical guide to adaptive light-sheet microscopy.

We describe the implementation and use of an adaptive imaging framework for optimizing spatial resolution and signal strength in a light-sheet microscope. The framework, termed AutoPilot, comprises hardware and software modules for automatically measuring and compensating for mismatches between light-sheet and detection focal planes in living specimens. Our protocol enables researchers to introduce adaptive imaging capabilities in an existing light-sheet microscope or use our SiMView microscope blueprint to set up a new adaptive multiview light-sheet microscope.

Imaging far and wide.

A custom-built objective lens called the Mesolens allows relatively large biological specimens to be imaged with cellular resolution.

Examining the Effects of Chromatic Aberration, Object Distance, and Eye Shape on Image-Formation in the Mirror-Based Eyes of the Bay Scallop Argopecten irradians.

The eyes of scallops form images using a concave spherical mirror and contain two separate retinas, one layered on top of the other. Behavioral and electrophysiological studies indicate that the images formed by these eyes have angular resolutions of about 2°. Based on previous ray-tracing models, it has been thought that the more distal of the two retinas lies near the focal point of the mirror and that the proximal retina, positioned closer to the mirror at the back of the eye, receives light that is out-of-focus.

Whole-animal functional and developmental imaging with isotropic spatial resolution.

Imaging fast cellular dynamics across large specimens requires high resolution in all dimensions, high imaging speeds, good physical coverage and low photo-damage. To meet these requirements, we developed isotropic multiview (IsoView) light-sheet microscopy, which rapidly images large specimens via simultaneous light-sheet illumination and fluorescence detection along four orthogonal directions. Combining these four views by means of high-throughput multiview deconvolution yields images with high resolution in all three dimensions.

Probing biological nanotopology via diffusion of weakly constrained plasmonic nanorods with optical coherence tomography.

Biological materials exhibit complex nanotopology, i.e., a composite liquid and solid phase structure that is heterogeneous on the nanoscale.

Role of HGF in epithelial-stromal cell interactions during progression from benign breast disease to ductal carcinoma in situ.

Introduction: Basal-like and luminal breast cancers have distinct stromal-epithelial interactions, which play a role in progression to invasive cancer. However, little is known about how stromal-epithelial interactions evolve in benign and pre-invasive lesions.

Methods: To study epithelial-stromal interactions in basal-like breast cancer progression, we cocultured reduction mammoplasty fibroblasts with the isogenic MCF10 series of cell lines (representing benign/normal, atypical hyperplasia, and ductal carcinoma in situ).

Motility-, autocorrelation-, and polarization-sensitive optical coherence tomography discriminates cells and gold nanorods within 3D tissue cultures.

We propose a method for differentiating classes of light scatterers based upon their temporal and polarization properties computed from time series of polarization-sensitive optical coherence tomography (PS-OCT) images. The amplitude (motility) and time scale (autocorrelation decay time) of the speckle fluctuations are combined with the cross-polarization pixel-wise to render Motility-, autocorrelation-, and polarization-sensitive (MAPS) OCT contrast images. This combination of metrics provides high specificity for discriminating diffusive gold nanorods and mammary epithelial cell spheroids within 3D tissue culture, based on their unique MAPS signature.

Longitudinal study of mammary epithelial and fibroblast co-cultures using optical coherence tomography reveals morphological hallmarks of pre-malignancy.

The human mammary gland is a complex and heterogeneous organ, where the interactions between mammary epithelial cells (MEC) and stromal fibroblasts are known to regulate normal biology and tumorigenesis. We aimed to longitudinally evaluate morphology and size of organoids in 3D co-cultures of normal (MCF10A) or pre-malignant (MCF10DCIS.com) MEC and hTERT-immortalized fibroblasts from reduction mammoplasty (RMF).

Monitoring airway mucus flow and ciliary activity with optical coherence tomography.

Muco-ciliary transport in the human airway is a crucial defense mechanism for removing inhaled pathogens. Optical coherence tomography (OCT) is well-suited to monitor functional dynamics of cilia and mucus on the airway epithelium. Here we demonstrate several OCT-based methods upon an actively transporting in vitro bronchial epithelial model and ex vivo mouse trachea.

Long-range alignment of gold nanorods in electrospun polymer nano/microfibers.

In this study, a scalable fabrication technique for controlling and maintaining the nanoscale orientation of gold nanorods (GNRs) with long-range macroscale order has been achieved through electrospinning. The volume fraction of GNRs with an average aspect ratio of 3.1 is varied from 0.

Imaging three-dimensional rotational diffusion of plasmon resonant gold nanorods using polarization-sensitive optical coherence tomography.

We demonstrate depth-resolved viscosity measurements within a single object using polarized optical scattering from ensembles of freely tumbling plasmon resonant gold nanorods (GNRs) monitored with polarization-sensitive optical coherence tomography. The rotational diffusion coefficient of the GNRs is shown to correlate with viscosity in molecular fluids according to the Stokes-Einstein relation. The plasmon resonant and highly anisotropic properties of GNRs are favorable for microrheological studies of nanoscale properties.

Magnetic and contrast properties of labeled platelets for magnetomotive optical coherence tomography.

This article introduces a new functional imaging paradigm that uses optical coherence tomography (OCT) to detect rehydrated, lyophilized platelets (RL platelets) that are in the preclinical trial stage and contain superparamagnetic iron oxides (SPIOs) approved by the U.S. Food and Drug Administration.

Magnetomotive optical coherence elastography for relating lung structure and function in Cystic Fibrosis.

Cystic fibrosis (CF) is a genetic defect in the cystic fibrosis transmembrane conductance regulator protein and is the most common life-limiting genetic condition affecting the Caucasian population. It is an autosomal recessive, monogenic inherited disorder characterized by failure of airway host defense against bacterial infection, which results in bronchiectasis, the breakdown of airway wall extracellular matrix (ECM). In this study, we show that the in vitro models consisting of human tracheo-bronchial-epithelial (hBE) cells grown on porous supports with embedded magnetic nanoparticles (MNPs) at an air-liquid interface are suitable for long term, non-invasive assessment of ECM remodeling using magnetomotive optical coherence elastography (MMOCE).