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Individual C. elegans animals in video frames are extracted by using routine image analysis techniques. Before image processing algorithms are applied, all indexed images are converted into grey images (Fig. 1A). A mean low-pass filter is then applied to smooth each grey image. This filter replaces every pixel with the average of its 3 3 neighborhood. Every image is subsequently thresholded and converted into a binary image in which objects are separated from the background by clear boundaries. To avoid time consuming computations, after the initial extraction of the area occupied by the animal, processing is restricted only to small boxes containing the animal rather than to the entire image.
To extract useful quantitative information about individual animals in a frame, a number of morphological operations are applied on the binary images . Dilation is one of the basic operators used and the basic effect of the operator is to gradually enlarge the boundaries of regions of foreground pixels. For labeling connected components in the image, every frame is scanned and pixels are grouped into components based on pixel connectivity. Large objects are assigned to animals in the image while smaller objects outside the perimeter of the animals are removed. Using built-in functions provided by the Image Analysis Toolbox of Matlab, the perimeter of each worm can be easily obtained in addition to the 'spine' (or 'skeleton') of the animal. We have also developed an algorithm to remove small and redundant 'branches' on the skeleton. The image processing procedure is summarized in Fig. 2 A more detailed description of the algorithm can be found in supplementary data [see Additional file 1].
We present, Nemo, an algorithm designed to measure and analyze nematode movement features by processing video image sequences. The system described here provides a powerful means of data extraction from 2D images. In conjunction with a GUI, Nemo constitutes an integrated approach to study nematode locomotion quantitatively by processing specific movement parameters and displaying measurable quantities. By enabling processing and reliable analysis of large amounts of data with high accuracy this system facilitates the systematic study and description of nematode behavior. While we only examined sinusoidal wild type animal movement to demonstrate the capacity of the tool, it can readily be utilized to handle complicated locomotion behaviors of both wild type and mutant animals, by introducing additional movement characteristics subject to quantification.
The area measurements were done with the help of the open source software Image J. After opening the images in Image J, calibration was done using the Set Scale option. Adjacent non-overlapping areas in the tunica adventitia in each section were selected and area measurements were done using the freehand selection Tool.19 On an average, four non-overlapping areas were chosen per specimen in order to cover the entire circumference of the artery. The VV number in all the selected areas of the specimen were visually calculated, and the number per unit area was later expressed as density. The mean VV density for a particular artery was calculated by taking the average of the densities obtained in all the specimens of the artery type.
Using our multiplex IHC module, we quantify immune cells and tumor cell markers across whole slide images. The tissue classifier add-on is employed to segment tumor and stroma and the spatial analysis module is used for proximity and invasive margin analysis.
Low magnification (5) plane-polarized light microscope images of (a) the buff-colored body of polychrome shard no. 10, (b) the buff-colored body of polychrome shard no. 48, (c) the buff-colored body of polychrome shard no. 49, (d) the gray-colored body of shard no. 52, (e) the gray-colored body of shard no. 62, (f) the gray-colored body of shard no. 83, (g) the red-colored body of shard no. 104, and (h) the red-colored body of shard no. 93
The matrix structure of the buff ware varied from hypocrystalline to a micro-granular containing fine sand and silt. In addition, in the buff ware, fine sand-sized grains consist of predominant quartz together with lower amounts of quartzite, felsic volcanic rock fragments, altered volcanic glass, feldspar, and biotite. Coarse sand-sized grains are comparatively less abundant and include trachytes, aphiric basalts, and carbonate rock fragments (limestone) (Fig. 5). Also, microscopic observations suggest that our samples of buff ware were generated from calcium (Ca)-rich clay, thereby revealing the calcareous nature of the original clay used for manufacturing these wares. SEM images and EDS micro-analysis of the cross-sections of the buff ware bodies revealed occasional scattered round-shaped pyroxene, plagioclase, and olivine crystals embedded in the matrix of vesicular volcanic glass (Fig. 6). The carbonates were present in fine grains. Large relicts of calcite were detected only rarely; the coarse grains of silicate rocks consisted of magmatic fragments, presumably of trachyte and andesite lithologies (Fig. 5).
Backscattered electron SEM images of local clay reveal (left) components including quartz, feldspar, and pyroxene within the matrix; (right) detailed image of a basaltic clast identified in the sample (no. 110) of local clay
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All the results shown were the average values obtained from at least three independently grown/processed lots of plants. Statistical analyses were processed using Microsoft Excel 2007, SPSS 17 and Origin 7.0 as detailed in every experiment. All images were processed using ImageJ 1.z32.
The values for relative bone volume and BMD were significantly decreased in mice from the group E. On the other hand, insignificant effects of subchronic alcohol consumption on relative bone volume without marrow cavity, bone surface and cortical bone thickness were observed. The results are summarized in Table 2. Representative reconstructed 3D images of the compact bone are illustrated in Fig. 2a, b.
1 2 3 10. Optical instruments and Microscopes Microscopes /Stereomicroscopes-Special microscopes 1020 1 E & OE. GENERAL CATALOGUE EDITION 17 Compact zoom stereomicroscope, SMZ-140-N2GGNEW! The Greenough optical system provides clear stereoscopic images ruggadized to operate in harsh environments of the laboratory or machines. - Binocular head, 45 inclined, 360 rotating - Widefield eyepieces WF10X/20mm - 4.1 Zoom ratio, WD=80mm - Magnification range: 10X-40X - Possible magnification with additional objectives of 3.5X up to 60X - N2GG: Base stand with pole and head holder - Black/white stage, Ø 80mm - Frosted glass stage plate, Ø 80mm - Intensity controlled halogen illumination - Incident 12V/15W and transmitted 12V/10W - Main supply 220V-240V (CE) Supplied with: Dust cover, eyecups, blue filter NEW! Type PK Cat. No. SMZ-140-N2GG 1 6.240 716 2 Digital Microscope for Schools/Laboratories, DM-1802-A - Widefield eyepiece WF10X/18mm - Built-in, digital imaging Chip - 1280 x 1024 Pixel resolution with USB2.0 output - 30 inclined, monocular viewing tube - Quadruple (4-place) nosepiece with click-Stop - Achromatic Objectives EA 4X, 10X, 40X (sprung) - Focussing Abbe condenser (N.A. 1.25) - Separate coarse and fine controls - Built-in mechanical stage with coaxial controls and slide holder - Adjustable 12V/20W halogen illumination - For 220-240V supplies, with plug (CE) - Motic Images Plus 2.0 ML software for PC (requires Win XP or later) - Motic Images Plus 2.0 ML software for Mac (requires Apple OSX or later) - Dust cover - Calibration slide Type Description PK Cat. No. DM-1802-A DM-1802-A with UK plug 3 Digital Stereomicroscopes, DM-143-FBGG-C - widefield objectives WF10X/20mm in a binocular, stereo head - built-in, digital chip - resolution: 2048 x 1536 Pixel, USB2.0 output - zoom Objectives 1X - 4X, Zoom factor 1:4 - compact column stand with wide, stable base - black/white stage plate - frosted glass stage plate - 12V/10W incident and transmitted halogen illumination with intensity control - for 100-240V supplies, with plug (CE) 1 1 Motic Motic 9.727 000 9.727 001 Supplied with: Motic Images Plus 2.0 (multilingual) software for PC (for Win XP or later) and for Mac (OSX or later), USB cable, dust cover, calibration slide. Type Description PK Cat. No. DM-143-FBGG-C DM-143-FBGG-C with UK plug 1 1 Motic 9.727 011 9.727 012 350c69d7ab