Stitching algorithms for biological specimen images

Abstract: In this paper, we address the problem of combining multiple overlapping image sections of biological specimens to obtain a single image containing the entire specimen. This is useful in the digitisation of a large number of biological specimens stored in museum collections and laboratories. In the case of many large specimens, it means that the specimen must be captured in overlapping sections instead of a single image. In this research, we have compared the performance of several known algorithms for this problem. In addition, we have developed several new algorithms based on matching the geometry (width, slope, and curvature) of the specimens at the boundaries. Finally, we compare the performance of a bagging approach that combines the results from multiple stitching algorithms. Our detailed evaluation shows that brightness-based and curvature-based approaches produce the best matches for the images in this domain

Advanced optical imaging in living embryos

Developmental biology investigations have evolved from static studies of embryo anatomy and into dynamic studies of the genetic and cellular mechanisms responsible for shaping the embryo anatomy. With the advancement of fluorescent protein fusions, the ability to visualize and comprehend how thousands to millions of cells interact with one another to form tissues and organs in three dimensions (xyz) over time (t) is just beginning to be realized and exploited. In this review, we explore recent advances utilizing confocal and multi-photon time-lapse microscopy to capture gene expression, cell behavior, and embryo development. From choosing the appropriate fluorophore, to labeling strategy, to experimental set-up, and data pipeline handling, this review covers the various aspects related to acquiring and analyzing multi-dimensional data sets. These innovative techniques in multi-dimensional imaging and analysis can be applied across a number of fields in time and space including protein dynamics to cell biology to morphogenesis

Methanol immersion reduces spherical aberration of water dipping lenses at long wavelengths used in multi-photon laser scanning microscopy

Dipping objectives were tested for multi-photon laser scanning microscopy, since their large working distances are advantageous for thick specimens and the absence of a coverslip facilitates examination of living material. Images of fluorescent bead specimens, particularly at wavelengths greater than 850 nm showed defects consistent with spherical aberration. Substituting methanol for water as the immersion medium surrounding the beads corrected these defects and produced an increase in fluorescence signal intensity. The same immersion method was applied to two representative biological samples of fixed tissue: mouse brain labeled with FITC for tubulin and mouse gut in which the Peyer’s patches were labeled with Texas Red bilosomes. Tissue morphology was well preserved by methanol immersion of both tissues; the two-photon-excited fluorescence signal was six times higher than in water and the depth of penetration of useful imaging was doubled. No modification of the microscope was needed except the provision of a ring to retain a sufficient depth of methanol for imaging

High resolution trichromatic road surface scanning with a line scan camera and light emitting diode lighting for road-kill detection

This paper presents a road surface scanning system that operates with a trichromatic line scan camera with light emitting diode (LED) lighting achieving road surface resolution under a millimeter. It was part of a project named Roadkills-Intelligent systems for surveying mortality of amphibians in Portuguese roads, sponsored by the Portuguese Science and Technology Foundation. A trailer was developed in order to accommodate the complete system with standalone power generation, computer image capture and recording, controlled lighting to operate day or night without disturbance, incremental encoder with 5000 pulses per revolution attached to one of the trailer wheels, under a meter Global Positioning System (GPS) localization, easy to utilize with any vehicle with a trailer towing system and focused on a complete low cost solution. The paper describes the system architecture of the developed prototype, its calibration procedure, the performed experimentation and some obtained results, along with a discussion and comparison with existing systems. Sustained operating trailer speeds of up to 30 km/h are achievable without loss of quality at 4096 pixels' image width (1 m width of road surface) with 250 µm/pixel resolution. Higher scanning speeds can be achieved by lowering the image resolution (120 km/h with 1 mm/pixel). Computer vision algorithms are under development to operate on the captured images in order to automatically detect road-kills of amphibians.This work was financed by FEDER Funds, through the Operational Programme for Competitiveness Factors-COMPETE, and by National Funds through FCT-Foundation for Science and Technology of Portugal, under the project PTDC/BIA-BIC/4296/2012 with the name-Roadkills: Intelligent systems for mapping amphibian mortality on Portuguese roads. C.S. and M.F. are supported by Research Grants contracts by FCT (UMINHO/BI/172/2013 and UMINHO/BI/175/2013 respectively). N.S. is supported by an IF (Investigador FCT) contract by FCT (IF/01526/2013). The authors also wish to thank the entities involved, in particular, School of Engineering of the University of Minho and the Algoritmi research center, the Faculty of Sciences of the University of Porto and the University Institute of Maia.info:eu-repo/semantics/publishedVersio

Bioimage informatics in the context of drosophila research

Modern biological research relies heavily on microscopic imaging. The advanced genetic toolkit of drosophila makes it possible to label molecular and cellular components with unprecedented level of specificity necessitating the application of the most sophisticated imaging technologies. Imaging in drosophila spans all scales from single molecules to the entire populations of adult organisms, from electron microscopy to live imaging of developmental processes. As the imaging approaches become more complex and ambitious, there is an increasing need for quantitative, computer-mediated image processing and analysis to make sense of the imagery. Bioimage informatics is an emerging research field that covers all aspects of biological image analysis from data handling, through processing, to quantitative measurements, analysis and data presentation. Some of the most advanced, large scale projects, combining cutting edge imaging with complex bioimage informatics pipelines, are realized in the drosophila research community. In this review, we discuss the current research in biological image analysis specifically relevant to the type of systems level image datasets that are uniquely available for the drosophila model system. We focus on how state-of-the-art computer vision algorithms are impacting the ability of drosophila researchers to analyze biological systems in space and time. We pay particular attention to how these algorithmic advances from computer science are made usable to practicing biologists through open source platforms and how biologists can themselves participate in their further development

Digital Image Correlation Of Heterogeneous Deformations In Polycrystalline Material With Electron Backscatter Diffraction

This work establishes the ability to conduct digital image correlation (DIC) investigations at varying length scales. DIC allows for a computational method of strain field measurements using multiple images to track random speckle patterns on material surfaces. The use of a powder silicon oxide speckle allows for high optical magnification correlation using conventional load frames. Self-assembling gold nanoparticles provide sub-micron resolution speckle patterns to study microstructure influences on deformation using scanning electron microscopy. The complex microstructure in aerospace grade aluminum and nickel-based superalloys, give rise to varied deformation fields, which can be studied using electron backscatter diffraction. Specimen preparation techniques, speckle patterns, and image correlation analysis are discussed. Experimental identification of strains at grain level can help validate computational crystal plasticity finite element models, which in turn provide better predictive computational models