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

Magnetic order in the quasi-two-dimensional easy-plane XXZ model

A Green's-function theory of antiferromagnetic short-range and long-range order (LRO) in the $S=1/2$ quasi-two-dimensional easy-plane XXZ model is presented. As the main new result, {\it two} phase transitions due to the combined influence of spatial and spin anisotropy are found, where below the higher and lower N\'{e}el temperature there occurs LRO in the transverse and in both the transverse and longitudinal spin correlators, respectively. Comparing the theory with neutron-scattering data for the correlation length of $\rm La_2CuO_4$, a very good agreement in the whole temperature dependence is obtained. Moreover, for $\rm La_2CuO_4$, $\rm Sr_2CuO_2Cl_2$, and $\rm Ca_{0.85}Sr_{0.15}CuO_2$ the second phase with longitudinal LRO is predicted to appear far below room temperature.Comment: 7 pages, 5 figure

Green's-function theory of the Heisenberg ferromagnet in a magnetic field

We present a second-order Green's-function theory of the one- and two-dimensional S=1/2 ferromagnet in a magnetic field based on a decoupling of three-spin operator products, where vertex parameters are introduced and determined by exact relations. The transverse and longitudinal spin correlation functions and thermodynamic properties (magnetization, isothermal magnetic susceptibility, specific heat) are calculated self-consistently at arbitrary temperatures and fields. In addition, exact diagonalizations on finite lattices and, in the one-dimensional case, exact calculations by the Bethe-ansatz method for the quantum transfer matrix are performed. A good agreement of the Green's-function theory with the exact data, with recent quantum Monte Carlo results, and with the spin polarization of a $\nu=1$ quantum Hall ferromagnet is obtained. The field dependences of the position and height of the maximum in the temperature dependence of the susceptibility are found to fit well to power laws, which are critically analyzed in relation to the recently discussed behavior in Landau's theory. As revealed by the spin correlation functions and the specific heat at low fields, our theory provides an improved description of magnetic short-range order as compared with the random phase approximation. In one dimension and at very low fields, two maxima in the temperature dependence of the specific heat are found. The Bethe-ansatz data for the field dependences of the position and height of the low-temperature maximum are described by power laws. At higher fields in one and two dimensions, the temperature of the specific heat maximum linearly increases with the field.Comment: 9 pages, 9 figure

New Perspectives in Sinographic Language Processing Through the Use of Character Structure

Chinese characters have a complex and hierarchical graphical structure carrying both semantic and phonetic information. We use this structure to enhance the text model and obtain better results in standard NLP operations. First of all, to tackle the problem of graphical variation we define allographic classes of characters. Next, the relation of inclusion of a subcharacter in a characters, provides us with a directed graph of allographic classes. We provide this graph with two weights: semanticity (semantic relation between subcharacter and character) and phoneticity (phonetic relation) and calculate "most semantic subcharacter paths" for each character. Finally, adding the information contained in these paths to unigrams we claim to increase the efficiency of text mining methods. We evaluate our method on a text classification task on two corpora (Chinese and Japanese) of a total of 18 million characters and get an improvement of 3% on an already high baseline of 89.6% precision, obtained by a linear SVM classifier. Other possible applications and perspectives of the system are discussed.Comment: 17 pages, 5 figures, presented at CICLing 201

Efficient Bayesian-based Multi-View Deconvolution

Light sheet fluorescence microscopy is able to image large specimen with high resolution by imaging the sam- ples from multiple angles. Multi-view deconvolution can significantly improve the resolution and contrast of the images, but its application has been limited due to the large size of the datasets. Here we present a Bayesian- based derivation of multi-view deconvolution that drastically improves the convergence time and provide a fast implementation utilizing graphics hardware.Comment: 48 pages, 20 figures, 1 table, under review at Nature Method

Three-dimensional femtosecond laser nanolithography of crystals

Nanostructuring hard optical crystals has so far been exclusively feasible at their surface, as stress induced crack formation and propagation has rendered high precision volume processes ineffective. We show that the inner chemical etching reactivity of a crystal can be enhanced at the nanoscale by more than five orders of magnitude by means of direct laser writing. The process allows to produce cm-scale arbitrary three-dimensional nanostructures with 100 nm feature sizes inside large crystals in absence of brittle fracture. To showcase the unique potential of the technique, we fabricate photonic structures such as sub-wavelength diffraction gratings and nanostructured optical waveguides capable of sustaining sub-wavelength propagating modes inside yttrium aluminum garnet crystals. This technique could enable the transfer of concepts from nanophotonics to the fields of solid state lasers and crystal optics.Comment: Submitted Manuscript and Supplementary Informatio

Iterative graph cuts for image segmentation with a nonlinear statistical shape prior

Shape-based regularization has proven to be a useful method for delineating objects within noisy images where one has prior knowledge of the shape of the targeted object. When a collection of possible shapes is available, the specification of a shape prior using kernel density estimation is a natural technique. Unfortunately, energy functionals arising from kernel density estimation are of a form that makes them impossible to directly minimize using efficient optimization algorithms such as graph cuts. Our main contribution is to show how one may recast the energy functional into a form that is minimizable iteratively and efficiently using graph cuts.Comment: Revision submitted to JMIV (02/24/13

A high-level 3D visualization API for Java and ImageJ

BACKGROUND: Current imaging methods such as Magnetic Resonance Imaging (MRI), Confocal microscopy, Electron Microscopy (EM) or Selective Plane Illumination Microscopy (SPIM) yield three-dimensional (3D) data sets in need of appropriate computational methods for their analysis. The reconstruction, segmentation and registration are best approached from the 3D representation of the data set. RESULTS: Here we present a platform-independent framework based on Java and Java 3D for accelerated rendering of biological images. Our framework is seamlessly integrated into ImageJ, a free image processing package with a vast collection of community-developed biological image analysis tools. Our framework enriches the ImageJ software libraries with methods that greatly reduce the complexity of developing image analysis tools in an interactive 3D visualization environment. In particular, we provide high-level access to volume rendering, volume editing, surface extraction, and image annotation. The ability to rely on a library that removes the low-level details enables concentrating software development efforts on the algorithm implementation parts. CONCLUSIONS: Our framework enables biomedical image software development to be built with 3D visualization capabilities with very little effort. We offer the source code and convenient binary packages along with extensive documentation at http://3dviewer.neurofly.de

Image-based Analysis of Patterns Formed in Drying Drops

Image processing and pattern recognition offer a useful and versatile method for optically characterizing drops of a colloidal solution during the drying process and in its final state. This paper exploits image processing techniques applied to cross-polarizing microscopy to probe birefringence and the bright-field microscopy to examine the morphological patterns. The bio-colloidal solution of interest is a mixture of water, liquid crystal (LC) and three different proteins [lysozyme (Lys), myoglobin (Myo), and bovine serum albumin (BSA)], all at a fixed relative concentration. During the drying process, the LC phase separates and becomes optically active detectable through its birefringence. Further, as the protein concentrates, it forms cracks under strain due to the evaporation of water. The mean intensity profile of the drying process is examined using an automated image processing technique that reveals three unique regimes: a steady upsurge, a speedy rise, and an eventual saturation. The high values of standard deviation show the complexity, the roughness, and inhomogeneity of the image surface. A semi-automated image processing technique is proposed to quantify the distance between the consecutive cracks by converting those into high contrast images. The outcome of the image analysis correlates with the initial state of the mixture, the nature of the proteins, and the mechanical response of the final patterns. The paper reveals new insights on the self-assembly of the macromolecules during the drying mechanism of any aqueous solution