Life Sciences Commons^™

Quantifying Planarian Behavior As An Introduction To Object Tracking And Signal Processing, Nicole C. Stowell, T. Goel, Vir Shetty , '22, Jocelyne Noveral, Eva-Maria S. Collins

Biology Faculty Works

Answers to mechanistic questions about biological phenomena require fluency in a variety of molecular biology techniques and physical concepts. Here, we present an interdisciplinary approach to introducing undergraduate students to an important problem in the areas of animal behavior and neuroscience—the neuronal control of animal behavior. In this lab module, students explore planarian behavior by quantitative image and data analysis with freely available software and low-cost resources. Planarians are ∼1–2-cm-long aquatic free-living flatworms famous for their regeneration abilities. They are inexpensive and easy to maintain, handle, and perturb, and their fairly large size allows for image acquisition with a webcam, …

Mapping Legume Roots Can Determine Best Performing Crops, Frédérique C. Guinel

Clear Language Summaries

Legume plants have a mutually beneficial relationship with bacteria. These beneficial bacteria live in nodules found on plant roots. Until recently there was no way to systematically measure the roots the nodules are found on and to place accurately the nodules on these roots. The research team created software and a method to measure multiple root parameters which were not available previously. This allows different plant varieties to be compared with precise measurements of the root structure in order to figure out which plants will grow better.

Detection Of Temporal Changes In Vegetative Cover On South Padre Island, Texas Using Image Classifications Derived From Aerial Color-Infrared Photographs, Ruben A. Mazariegos, Kenneth R. Summy, Frank W. Judd, Robert I. Lonard, James H. Everitt

Physics and Astronomy Faculty Publications and Presentations

Supervised image classifications developed from 23 x 23 cm aerial color-infrared aerial photographs (1:5,000 scale) were used to evaluate temporal changes in vegetative cover occurring within three 150 x 300-m research sites on South Padre Island, Texas. Use of high-resolution digitized imagery (ground pixel resolution of ca. 0.1 m) and survey-grade GPS for positional measurements of ground control points (20-25 1.0m2 targets within each research site) resulted in consistently high levels of geometric accuracy, with root mean square errors (RMSEs) ranging between 0.397 – 2.867. Similarly, use of relatively simple information categories (dry and wet sand, live and dead vegetative …

Mcnamara 2011 Feature Extraction (Image Analysis), George Mcnamara

George McNamara

Feature Extraction presentation and movies in a ZIP file from a presentation I gave at ISAC 2011 in Baltomore, Md.

Feature extraction is one phrase for image analysis.

Use Of Archive Aerial Photography For Monitoring Black Mangrove Populations, James H. Everitt, C. Yang, Frank W. Judd, Kenneth R. Summy

Biology Faculty Publications and Presentations

A study was conducted on the South Texas Gulf Coast to evaluate archive aerial color-infrared (CIR) photography combined with supervised image analysis techniques to quantify changes in black mangrove [Avicennia germinans (L.) L.] populations over a 26-year period. Archive CIR film from two study sites (sites 1 and 2) was studied. Photographs of site 1 from 1976,1988, and 2002 showed that black mangrove populations made up 16.2%, 21.1%, and 29.4% of the study site, respectively. Photographs of site 2 from 1976 and 2002 showed that black mangrove populations made up 0.4% and 2.7% of the study site, respectively. Over the …

Spectral Reflectance And Digital Image Relations Among Five Aquatic Weeds, James H. Everitt, Kenneth R. Summy, Chenghai Yang

Biology Faculty Publications and Presentations

This study reports on the use of an artificial quartz halogen lighting source to facilitate the acquisition of spectral light reflectance measurements and digital imaging of invasive aquatic weeds. Spectral leaf or leaf/stem reflectance measurements were made on five aquatic weeds: Eurasian watermilfoil (Myriophyllum spicatum L.), hydrilla [Hydrilla verticillata (L. F.) Royle], parrotfeather [Myriophyllum aquaticum (Vall.), waterhyacinth [Eichhornia crassipes (Mart.) Solms], and waterlettuce (Pistia stratiotes L.). Reflectance measurements were studied at five wavelengths of the electromagnetic spectrum: 450 nm (visible blue), 550 nm (visible green), 650 nm (visible red), 680 nm (visible red edge), and 850 nm (near-infrared). Reflectance values …

Spots Of Adult Male Red-Spotted Newts Are Redder And Brighter Than In Females: Evidence For A Role In Mate Selection?, Andrew K. Davis, Kristine L. Grayson

Biology Faculty Publications

As aquatic adults, eastern red-spotted newts (Notophthalmus v. viridescens) are generally green with two rows of dorsal spots, which vary in number between individuals and range in colour from orange to red. The function of these spots is unknown, but it is possible that they serve as sexual ornamentations and we examined this hypothesis by testing for sexual dimorphism in spot characteristics. We used an image analysis approach that has been used previously with this and other amphibian species to compare the number, size and colour – redness (hue score) and brightness – of spots in 100 male …

Improving Natural History Research With Image Analysis: The Relationship Between Skin Color, Sex, Size And Stage In Adult Red-Spotted Newts, Andrew K. Davis, Kristine L. Grayson

Biology Faculty Publications

Natural history researchers are increasingly using digital cameras and computer software to measure their study animals. Adult Red-spotted Newts (Notophthalmus viridescens viridescens) are known to display a range of skin colors, from brown to green, but it has not been possible to quantify this variation until the advent of image analysis technology. We used an image analysis approach to compare skin color between sexes, across a range of sizes, and between aquatic and post-breeding (emigrating to the terrestrial habitat) stage adult newts. From 232 individuals (53% male, 47% female) we documented a wide but subtle range of skin …

Mgo·1.5al2o3 Spinel Grain Growth And Microstructure Characterization By Scanning Electron Microscopy And Digital Image Analysis, G. Bonifazi, E. Proverbio

Scanning Microscopy

The microstructure of sintered polycrystalline MgO·1.5Al₂O₃ ceramic is strongly affected by the sintering conditions due to the precipitation of α-alumina at a temperature lower than about 1400°C. Consequently, the mechanical properties, depending on grain size distribution, are greatly influenced. Three different microstructures were obtained by a two step sintering process adopting an intermediate sintering temperature of 1050°C, 1100°C and 1300°C respectively, and a final sintering temperature of 1500°C. Comparable samples obtained directly by firing at 1500°C were used. Digital image analysis (DIA) carried out on scanning electron microscope (SEM) images was performed in order to better describe …

Present Developments In Image Analysis, Peter Smart, Xiaoling Leng

Scanning Microscopy

The paper discusses novel methods of analysing oriented textures, explains some of the problems which had to be overcome to make these methods work, and indicates where future developments might be expected. This has required improvements in the methods of intensity gradient analysis, the development of large filter methods for mapping features defined in terms of their texture, and the introduction of ideas from the theory of regionalised variables.

The Effect Of Varying Environmental Conditions On Phytolith Morphometries In Two Species Of Grass (Bouteloua Curtipendula And Panicum Virgatum), T. B. Ball, J. D. Brotherson

Scanning Microscopy

Solid deposits of SiO₂ (phytoliths) accumulate in many plants in specific intracellular and extracellular locations. Phytoliths have morphological characteristics unique to some taxa and therefore have taxonomic significance. Phytoliths persist and maintain their morphological integrity long after a plant has died, thus becoming a microfossil of the plant that produced them. Development of phytolith sytematics for microfossil phytoliths has traditionally followed a typological approach based on simple verbal descriptions of shape. A new method for use in phytolith sytematics is the morphometric approach which employs computer-based Image Analysis Systems to make quantified measurements of morphological parameters (size, shape, texture, …

Quantitative Imaging Ion Microscopy: A Short Review, G. A. Valaskovic, G. H. Morrison

Scanning Microscopy

A short review of recent efforts being made in the quantification of images in ion microscopy is given. Special aspects of instrumentation, detection and acquisition, which are unique to direct imaging secondary ion mass spectrometry, are discussed in relation to the successful application of traditional empirical quantification schemes. Application of such quantification schemes requires proper sample preparation, standardization, analysis, and quite often, special techniques in image processing and the correlation of ion microscopy with other microscopies. Quantification within this technique is a difficult goal which can only be realized if the analyst pays strict attention to every step of the …

Some Applications Of Image Analysis To Materials Science, François Grillon

Scanning Microscopy

We have presented four applications of Image Analysis to material science. The first one is on a yarn composite SiC where we want to know the relative proportion of matrix, fibers, porosity and the size of the fibers. The results are used to estimate mechanical properties of the composite.

The second one is to measure the residual porosity after a laser shock on powder metallurgy steel. The knowledge of the depth of the affected zone is necessary to optimise the laser treatment.

The third one uses Fourier transformation to analyse plastic deformation on grains. Values are obtained from Fourier transform …

Processing Multi-Spectral Scanning Electron Microscopy Images For Quantitative Microfabric Analysis, N. K. Tovey, D. L. Dent, W. M. Corbett, D. H. Krinsley

Scanning Microscopy

Multi-spectral image analysis is a powerful method to characterise quantitatively the mineralogy and microfabric of soils, sediments, and other particulate materials. Backscattered scanning electron microscope (SEM) images of polished, resin-impregnated samples are grouped with the corresponding X-ray elemental maps using classification methods commonly used in remote sensing. However, the resulting mineral-segmented images require processing to render them suitable for quantification. In the past, this has been done subjectively and interactively, but the new objective methods described in this paper largely eliminate this subjectivity. An intensity gradient magnitude image of the original backscattered electron image is used as the basis of …

Morphological Filtering And Granulometric Analysis On Scanning Electron Micrographs: Applications In Materials Science, Murielle Prod'homme, Michel Coster, Liliane Chermant, Jean-Louis Chermant

Scanning Microscopy

For many applications, scanning electron microscopy (SEM) images reflect the granular texture of analysed objects. So it is important to characterise the morphology of this texture and also to filter these images. Because the size of the texture is the main criterion to be studied, we have focused our paper on granulometric analysis.

We present basic parameters, morphological filtering and granulometry for Rⁿ•R functions and their properties with local knowledge and anamorphosis.

Some applications in the domain of materials science illustrate these methods and present their suitable possibilities.

Preparation And Characterization Of Some Particulate Materials In The Aluminum Industry, A. Csordás-Tóth, B. Szikora, J. Kürthy-Komlósy, I. Tassy

Scanning Microscopy

Preparation and characterization techniques for the following particulate materials are reviewed: micromineralogical samples of bauxite, alumina and its trihydroxide, as well as sedimentary and respirable particles. Scanning electron microscopy (SEM), energy dispersive X-ray microanalysis (EDS) and image analysis were used to characterize the microminerals of bauxite. Comparisons were made among micromineralogical samples with various grain size fractions and the degree of weathering could be quantified. Programs were developed for characterization of the sandy and floury types of aluminum trihydroxide and alumina. We have used backscattered electron SEM images to characterize the size and shape of various aluminum trihydroxides. Comparison could …

The Study Of The Surface Geometry Of Renal Stone Fragments After Shock Wave And Ultrasound Disintegration, Roch Thibert, Rashad Tawashi

Scanning Microscopy

Computerized image analysis was used for characterizing the irregular boundaries of calcium oxalate stone fragments resulting from shock wave and ultrasound disintegration. The complexity of the contour of the fragments was determined to evaluate the surface roughness of the rugged profile of the samples. Crack propagation on the crystal surface of the mineral phase was studied using fractal geometry. A significant difference was observed in the boundary variation of the calcium oxalate stone fragments treated by shock wave and ultrasound. Crack propagation in the mineral phase crystal was found to depend on the method of fragmentation used. There is also …

Bone Ingrowth Into Porous Coated Canine Total Hip Replacements. Quantification By Backscattered Scanning Electron Microscopy And Image Analysis, Murali Jasty, Charles R. Bragdon, Steven Schutzer, Harry Rubash, Teresa Haire, William H. Harris

Scanning Microscopy

Bone ingrowth into titanium fiber mesh porous-surfaced canine total hip replacement prostheses was evaluated and quantified using a computer assisted image analysis system attached to a scanning electron microscope equipped with a back scattered electron detector. Excellent contrast between the bone, the porous metal and the soft tissues resulted in the backscatter mode, allowing easy differentiation of these components in real time by the image analysis based on gray scales. By three weeks the mean (± standard deviation) amount of bone ingrowth expressed as a percentage of porous layer measured 7.2% (± 1.5%) for the acetabular components, and 3.9% (± …

Bovine Aorta Endothelial Cell Incubation With Interleukin 2: Morphological Changes Correlate With Enhanced Vascular Permeability, Corazon D. Bucana, Joann Trial, Audrey C. Papp, Kenneth K. Wu

Scanning Microscopy

Interleukin 2 induced alterations in the morphology of bovine aortic endothelial cells in vitro. The changes observed in confluent cultures of bovine aortic endothelial cells included retraction and elongation of eel ls leading to enlarged gaps between cells quantified by image analysis. Purified IL-2 (1 U/ml medium) increased the gaps between endothelial cells 3-4-fold compared with control cultures. The effect was transient, since the cells reverted to their original morphology 6-12 hours after the removal of lL-2. Correlative scanning electron microscopy (SEM) studies using fresh bovine aorta showed a dose-dependent alteration of the endothelial surface by IL-2 characterized by rounding …

The Capabilities Of The Microprobe Kontron Image Analysis System: Application To Mineral Beneficiation, W. Petruk

Scanning Microscopy

Image analysis is a technique for determining quantities, grain size distributions, grain orientations, intergrowths, associations, liberations and degrees of alteration of minerals or phases in naturally occurring and processed materials. It is performed by analysing images of polished or thin sections of the material under study. To obtain accurate results the images must be faithful reproductions of the material, and each mineral or phase displayed in the images must be distinct enough to be automatically discriminated and identified without operator interaction. An image analysis system that meets these requirements was developed in the Process Mineralogy Section at CANMET by interfacing …

Extraneous Background-Correction Program For Matrix Bound Multiple Point X-Ray Microanalysis, W. C. De Bruijn, M. P. C. Van Miert

Scanning Microscopy

A program is described that allows online determination of extraneous background in multiple point X-ray microanalytical matrices. The program is based upon the calculations of the extraneous background for the film (when present), the standard and the unknown by (100 sec.) point analysis. The program searches for a peak-free part of the spectrum in which the calculated value for the extraneous background is about equal to the value in this region of the spectrum (=b_e). Online the contents of this b_e-region is subtracted from an unmanipulated continuum region in the vicinity of the element present in …

Image Analysis And X-Ray Microanalysis In Cytochemistry, W. C. De Bruijn, H. K. Koerten, M. I. Cleton-Soeteman, C. J. G. Blok-Van Hoek

Scanning Microscopy

When cytochemical reaction products are homogeneously distributed within an organelle, point analyses suffice for the quantitative approach. However, quantitative analysis becomes tedious, when the elements in the reaction product are inhomogeneously distributed. Problems arise when elements from two reaction products have to be related to each other, or to endogenous cytological products (ferritin, haemosiderin, calcium, electron dense markers), either topographically or in concentration. When analyzing inhomogeneous/heteromorphical reaction product-containing organelles special attention has to be paid to measure and relate both volume and concentration. In this paper a relative simple structure (eosinophil granules) is chosen to demonstrate that the acquisition of …

Application Of Chelex Standard Beads In Integrated Morphometrical And X-Ray Microanalysis, W. C. De Bruijn, M. I. Cleton-Soeteman

Scanning Electron Microscopy

Chelex ion exchange beads loaded with a known amount (18.3% weight percentage (w/w)) of platinum, have been co-embedded with a mouse peritoneal cell population. To establish the influence of the various deconvolution methods applied, upon the platinum concentration in cytoplasmic granules and erythrocytes these cross-sectioned beads are used as a standard. It is concluded that irrespective of the deconvolution method chosen 1) the Pt concentration inside the particles is identical when the particles and the co-embedded Chelex Pt standard, are analysed strictly under the same instrumental conditions 2) the Pt concentration outside the particle is zero, or virtually zero when …

Integration Of X-Ray Microanalysis And Morphometry Of Biological Material, W. C. De Bruijn

Scanning Electron Microscopy

It was investigated how to extract both morphometrical and X-ray elemental information from scanning electron microscopical (SEM) or scanning transmission electron microscopical (STEM)-images and how to integrate these two information streams either on line or off-line after storage.

Cytochemical reaction products in cell organelles in ultrathin sections are the biological structures of interest. In such organelles four different situations can be met: morphologically the structures are homomorph or heteromorph; chemically the elements are distributed either homogeneously or heterogeneously. A new program has been proposed and described, which permits determination of both the area and the mean net-intensity value of chemical …

A Rapid Technique For Counting Cracks In Rocks, W. B. Durham, J. M. Beiriger, H. C. Weed

Scanning Electron Microscopy

Using a scanning electron microscope (SEM) and an image analyzer, we have developed a technique for counting and measuring cracks in rocks which is more efficient than traditional techniques in which an operator performs all image analysis functions. The key aspect of the technique is that black-on-white tracings of fresh cracks, which can be made rather rapidly by an operator, are measured and digitized by an image analyzer. The most time-consuming step in the process has now become the generation of SEM micrographs and pertinent chemical (mineralogical) information, not the quantification of crack structure. The technique has been applied to …

Interactive Image Processing For Electron Microscopy: Matching Hardware With Software, W. O. Saxton

Scanning Electron Microscopy

The image processing techniques used 'a posteriori' to extract information from electron micrographs are surveyed, including particularly image averaging, selective averaging, 3-D reconstruction, and high resolution focal series restoration; recent developments in online image pick up and control have led to fully automatic focussing, stigmating and alignment by a frame store system equipped with a real time correlator board. The diversity of the techniques encountered calls for large integrated program systems with flexible command languages; however, a dilemma exists between providing the user with convenient control of special hardware facilities such as frame stores and array processors, and preventing the …