OpenSPIM - an open access platform for light sheet microscopy

Light sheet microscopy promises to revolutionize developmental biology by enabling live in toto imaging of entire embryos with minimal phototoxicity. We present detailed instructions for building a compact and customizable Selective Plane Illumination Microscopy (SPIM) system. The integrated OpenSPIM hardware and software platform is shared with the scientific community through a public website, thereby making light sheet microscopy accessible for widespread use and optimization to various applications.Comment: 7 pages, 3 figures, 6 supplementary videos, submitted to Nature Methods, associated public website http://openspim.or

Video-rate volumetric neuronal imaging using 3D targeted illumination

Fast volumetric microscopy is required to monitor large-scale neural ensembles with high spatio-temporal resolution. Widefield fluorescence microscopy can image large 2D fields of view at high resolution and speed while remaining simple and costeffective. A focal sweep add-on can further extend the capacity of widefield microscopy by enabling extended-depth-of-field (EDOF) imaging, but suffers from an inability to reject out-of-focus fluorescence background. Here, by using a digital micromirror device to target only in-focus sample features, we perform EDOF imaging with greatly enhanced contrast and signal-to-noise ratio, while reducing the light dosage delivered to the sample. Image quality is further improved by the application of a robust deconvolution algorithm. We demonstrate the advantages of our technique for in vivo calcium imaging in the mouse brain.This work was funded by the National Institutes of Health (R21EY026310) and the National Science Foundation (CBET-1508988). The authors wish to thank E. McCarthy and Prof. M.J. Baum for providing mouse brain slices used in this manuscript, and A. I. Mohammed for providing in vivo mouse brain samples in the early stages of this work. (R21EY026310 - National Institutes of Health; CBET-1508988 - National Science Foundation)Published versio

Preferential concentration of inertial sub-kolmogorov particles. The roles of mass loading of particles, Stokes and Reynolds numbers

Turbulent flows laden with inertial particles present multiple open questions and are a subject of great interest in current research. Due to their higher density compared to the carrier fluid, inertial particles tend to form high concentration regions, i.e. clusters, and low concentration regions, i.e. voids, due to the interaction with the turbulence. In this work, we present an experimental investigation of the clustering phenomenon of heavy sub-Kolmogorov particles in homogeneous isotropic turbulent flows. Three control parameters have been varied over significant ranges: $Re_{\lambda} \in [170 - 450]$, $St\in [0.1 - 5]$ and volume fraction $\phi_v\in [2\times 10^{-6} - 2\times 10^{-5}]$. The scaling of clustering characteristics, such as the distribution of Vorono\"i areas and the dimensions of cluster and void regions, with the three parameters are discussed. In particular, for the polydispersed size distributions considered here, clustering is found to be enhanced strongly (quasi-linearly) by $Re_{\lambda}$ and noticeably (with a square-root dependency) with $\phi_v$, while the cluster and void sizes, scaled with the Kolmogorov lengthscale $\eta$, are driven primarily by $Re_{\lambda}$. Cluster length $\sqrt{\langle A_c \rangle}$ scales up to $\approx 100 {\eta}$, measured at the highest $Re_{\lambda}$, while void length $\sqrt{\langle A_v \rangle}$ scaled also with $\eta$ is typically two times larger ($\approx 200 {\eta}$). The lack of sensitivity of the above characteristics to the Stokes number lends support to the "sweep-stick" particle accumulation scenario. The non-negligible influence of the volume fraction, however, is not considered by that model and can be connected with collective effects

Calipso: Physics-based Image and Video Editing through CAD Model Proxies

We present Calipso, an interactive method for editing images and videos in a physically-coherent manner. Our main idea is to realize physics-based manipulations by running a full physics simulation on proxy geometries given by non-rigidly aligned CAD models. Running these simulations allows us to apply new, unseen forces to move or deform selected objects, change physical parameters such as mass or elasticity, or even add entire new objects that interact with the rest of the underlying scene. In Calipso, the user makes edits directly in 3D; these edits are processed by the simulation and then transfered to the target 2D content using shape-to-image correspondences in a photo-realistic rendering process. To align the CAD models, we introduce an efficient CAD-to-image alignment procedure that jointly minimizes for rigid and non-rigid alignment while preserving the high-level structure of the input shape. Moreover, the user can choose to exploit image flow to estimate scene motion, producing coherent physical behavior with ambient dynamics. We demonstrate Calipso's physics-based editing on a wide range of examples producing myriad physical behavior while preserving geometric and visual consistency.Comment: 11 page

Precise multimodal optical control of neural ensemble activity.

Understanding brain function requires technologies that can control the activity of large populations of neurons with high fidelity in space and time. We developed a multiphoton holographic approach to activate or suppress the activity of ensembles of cortical neurons with cellular resolution and sub-millisecond precision. Since existing opsins were inadequate, we engineered new soma-targeted (ST) optogenetic tools, ST-ChroME and IRES-ST-eGtACR1, optimized for multiphoton activation and suppression. Employing a three-dimensional all-optical read-write interface, we demonstrate the ability to simultaneously photostimulate up to 50 neurons distributed in three dimensions in a 550 × 550 × 100-µm3 volume of brain tissue. This approach allows the synthesis and editing of complex neural activity patterns needed to gain insight into the principles of neural codes

Paired-angle-rotation scanning optical coherence tomography forward-imaging probe

We report a novel forward-imaging optical coherence tomography (OCT), needle-probe paired-angle-rotation scanning OCT (PARS-OCT) probe. The probe uses two rotating angled gradient-index lenses to scan the output OCT probe beam over a wide angular arc (∼19° half-angle) of the region forward of the probe. Among other advantages, this probe design is readily amenable to miniaturization and is capable of a variety of scan modes, including volumetric scans. To demonstrate the advantages of the probe design, we have constructed a prototype probe with an outer diameter of 1.65 mm and employed it to acquire four OCT images, with a 45° angle between adjacent images, of the gill structure of a Xenopus laevis tadpole. The system sensitivity was measured to be 93 dB by using the prototype probe with an illumination power of 450 μW on the sample. Moreover, the axial and the lateral resolutions of the probe are 9.3 and 10.3-12.5 μm, respectively

Environmental sensitivity of n-i-n and undoped single GaN nanowire photodetectors

In this work, we compare the photodetector performance of single defect-free undoped and n-in GaN nanowires (NWs). In vacuum, undoped NWs present a responsivity increment, nonlinearities and persistent photoconductivity effects (~ 100 s). Their unpinned Fermi level at the m-plane NW sidewalls enhances the surface states role in the photodetection dynamics. Air adsorbed oxygen accelerates the carrier dynamics at the price of reducing the photoresponse. In contrast, in n-i-n NWs, the Fermi level pinning at the contact regions limits the photoinduced sweep of the surface band bending, and hence reduces the environment sensitivity and prevents persistent effects even in vacuum

Development of an in-field tree imaging system : a thesis presented in partial fulfilment of the requirements for the degree of Master of Technology at Massey University

Quality inventory information is essential for optimal resource utilisation in the forestry industry. In-field tree imaging is a method which has been proposed to improve the preharvest inventor assessment of standing trees. It involves the application of digital imaging technology to this task. The method described generates a three dimensional model of each tree through the capture of two orthogonal images from ground level. The images are captured and analysed using the "TreeScan" in-field tree imaging system. This thesis describes the design, development, and evaluation of the TreeScan system. The thesis can also be used as a technical reference for the system and as such contains appropriate technical and design detail. The TreeScan system consists of a portable computer, a custom designed high resolution scanner with integral microcontroller, a calibration rod, and custom designed processing software. Images of trees are captured using the scanner which contains a CCD line scan camera and a precision scanning mechanism. Captured images are analysed on the portable computer using customised image processing software to estimate real world tree dimensions and shape. The TreeScan system provides quantitative estimates of five tree parameters; height, sweep, stem diameter, branch diameter, and feature separation such as internodal distance. In addition to these estimates a three dimensional model is generated which can be further processed to determine the optimal stem breakdown into logs