Consists of a partial identity model that improves the probabilistic identity associations among samples. SPIM employs the spatial location where samples were collected to proceed. It resolves the uncertainty in individual identities by capitalizing on two key ecological spatial concepts: population density and home range size. This tool can improve density determination into the categorical spatial mark-resight (SMR) model.
Provides a fully automated video analysis tool for counting worms in two regions. WormTrapAssay evaluates videos from trap assays, extracts time-lapse images from a video and binarizes the images using local adaptive thresholding. The software displays the number of worms in each trap for each image. This module is part of the QuantWorm software.
Counts worms, especially in a context of chemotaxis. WormCounter offers to users the possibility to choose image processing or manual inspection. Image processing enables batch analysis of multiple well or plate images. Manual inspection allows users to review the result of image analysis and adjusts errors in fully automated analysis. This module is part of the QuantWorm software.
Calculates the number and the size of seeds thank to a white paper sheet of standard size as a background. SeedCounter automates evaluation of phenotypic parameters of grains using mobile devices running the Android operational system. It is efficient and sufficiently accurate for the large-scale analysis of phenotypic characteristics in wheat grains. The tool converts pixels into the metric scale to estimate the output values.
Allows image capture and analysis for measurement of cereal grain size and colour. GrainScan uses utilizes reflected light to capture colour information described in a device independent colour space (CIELAB), allowing comparison of colour data between scanning devices. The software enables the standardized study of grain size, shape and colour. It can be can be implemented for many different plant species that also have regular, approximately elliptical morphology.
Discovers the colony area percentage and an intensity weighted colony area percentage from flatbed scanner acquired images of colony formation assays conducted in multi-well plates. ColonyArea precisely quantifies scanned images of colony formation assays. It employs information about the plate type and the number of selected wells to build a mask that will set the intensity of the pixels belonging to the space in between wells to zero.
Enumerates clustered circular objects such as bacterial colonies. OpenCFU can handle digital pictures as well as live stream from a video device/webcam. This software is cross-platform, fast, reliable and allows the user to implement intuitive filters. It was shown to be very accurate and, with high definition pictures, did not generate more errors than the average human error. Finally, OpenCFU provides postprocessing filters to eliminate detected objects according to their intensity and colour similarity. This makes the method even more robust since it can be used to exclude circular artefacts such as contaminant bacteria.
Counts eggs from a captured image. WormEgg is based on a parameter-free detection algorithm which consist of five main steps: (1) identifying single egg objects; (ii) determining valid egg detection parameters; (iii) applying multiple thresholds; (iv) analyzing morphology of detected objects and (v) removing duplicate findings. This module is part of the QuantWorm software.
Analyzes C. elegans lifespan, locomotion, body size, and egg laying assay phenotypes. QuantWorm contains several components for image acquisition and image analysis that provides multiple measurements on C. elegans. This software can be easily modified by developers to adapt methods from several popular systems. It can be used with a microscope equipped with a digital camera and motorized stage.
Scores C. elegans on agar plates for mortality, size, and fecundity. WormScan is an automated software system using photo scanners. It can replace manual counting of worm populations and score of survival. An archival record is automatically stored as a compressed image file on which identified worms are highlighted.
Provides image and video processing algorithms in a processing framework. VIAME is a computer vision library targeting marine species analytics. It integrates a modular dataflow architecture that enables straightforward integration of a wide variety of third party analytics, libraries and tools. This application is based on KWIVER, the Kitware Video and Image Exploitation and Retrieval toolkit. It can also be used as a general computer vision toolkit.
Allows users to measure nematode chemotaxis behavior and features in a browser. NemaCount is available as a Google Chrome Extension and offers a suite of functions that aim to measure and analyze diverse nematode behaviors including chemotaxis, odortaxis, avoidance, and thermotaxis assays. The purpose of this tool is to provide a method for analyzing nematode behavior that could especially be used by researchers to Caenorhabditis elegans research.
Analyzes photographs of potato crop samples in field. PotatoSize works with a photograph of a sample dig. This software allows users to know how to carry out the dig, arrange the sample potatoes and take the photograph.
Permits scientific evaluation of 2D images. GSA Image Analyser is a program that allows (1) automatic surface calculation of the surfaces of all recognized objects, (2) direct length calculation of very complex and very ramified objects, and (3) object counting with an automatic count-function, a grid-intersection-count-function and two manual count-procedures.
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