Consists of a cloud based deep learning solution for image segmentation of light, electron and X-ray microscopy. CDeep3M serves for image segmentation tasks of large and complex 2D and 3D microscopy datasets by taking advantage of the underlying architecture of a deep learning convolutional neural network (CNN) called DeepEM3D. This software is also available on the Amazon Web Services (AWS) platform.
Serves for effective segmentation of multidimensional datasets. MIB can recognize several number of imaging formats and offers a variety of image processing tools. It also simplifies utilization and quantification of acquired data. It permits users to segment large datasets, to realize 3D visualization, and to quantify images and models. Its parameters enable users to insert plugin s to customize the program for specific needs.
Allows acquisition and evaluation of high-quality images of plants that had been raised in standard laboratory conditions. GROWSCREEN incorporates standard procedures of single-image processing with an automated setup. It allows recognition of light-induced growth acclimation responses within 24 h. This tool can be useful for ecophysiology studies and to analyse effects of agrochemicals or xenobiotica as well as differences between plant lines caused by their varying genetic backgrounds.
Allows users to perform automated image analysis of plant roots. RootGraph is a method that employs a weighted graph-based optimization step to produce an automated, primary root identification procedure. It is able to estimate the number, length, and diameter of roots and can separate primary roots from lateral roots. This tool can quantify traits for each primary root as well as each primary root’s associated lateral roots, but can do so under high-throughput conditions.
Provides a semi-automatically segmented images application. Seascape is designed to obtain images from underwater photographs of benthic communities, where each individual patch (such as species, functional groups, substratum types or any sessile cover categories) is routinely associated to its areal cover and perimeter. This method allows pixels to be grouped into segments and then classified based on user-defined classes.
Provides a package of scripts for analysis and selection of in situ images of embryo. Isimage includes two primary algorithms: (1) embryo-masking through image segmentation to split the part of the image containing the embryo that forms the image background; and (2) color-separation within embryo outline to detect the approximate hues of in situ stain, and pigmented and un-pigment embryo in each image.
Serves for the high-throughput analysis of root system architecture. GiA Roots estimates root system architecture (RSA) traits from a large number of root system images and identify roots from the background, i.e., segmenting the image. It includes: an optional userassisted processing of images, scale calibration, trait selection, image segmentation, and trait measurement.
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.
Calculates the stained areas in a Masson Trichrome stained slide as well as the adipose tissue area. FibroQuant is a method for systematic high resolution digital quantification of different tissue types in the heart. This method of fibrosis quantification can be used for several applications like the determination of the fibrosis pattern in the heart could provide an important link for genotype-phenotype relationships in genetic cardiomyopathies.
Assists users to analyze large-scale image data. This program offers several functionalities such as: acquisition of plant images, transformation of amounts of real-time image data to numerical data, and presentation of these data as graphs. This system can be used by plant biologists and data are automatically acquired and processed. Moreover, this software enables tracking of plant growth.
Handles image processing for analyze of Drosophila larval locomotion. MagRecognizer processes a video file to create a list of coordinates of 13 points identified along the midline of an animal. This tool exploits the record of stage coordinates created by the WormTracker software to process the position of the animal on the plate. This module is a component of the MaggotTracker software.
Enables to interactively segment images and assign semantic annotations to those segments. AISO gives to researchers the opportunity to increase the computational value of image data via the annotation feature. The data-enhanced images can be utilized to mine biological data sets, train machine-learning software, and generate conclusions via semantic inference. This software can be useful for biology researchers and scientific journals that are interested in adding annotated images and metadata to their publication pipeline.
Captures the mass spectrometry (MS) lesion spatial distribution and identifies lesions regardless of their orientation, shape or size. RMNMS detects MS lesions using a training library containing T2-weighted (T2W) and FLAIR images along with manual T2W lesion masks. Moreover, it assists users in the detection of presence of lesions as lesion-wise measures.
Segments nearly elliptic objects via parametric active contour. E-Snake applies an active contour (named snake) segmentation method by using exponential splines as basis functions to represent the outline of the shape. This ImageJ plugin emulates elliptical and circular shapes and can produce an approximation of any closed curve in the plane. These proprieties can be useful to delineate cross sections of cylindrical-like conduits and to outline blob-like objects.
Provides a deep learning-based solution for angiodysplasia lesions segmentation from video capsule endoscopy. Angiodysplasia Detection and Localization, which is based on a modification of the U-Net model, enables the prediction of angiodysplasia lesions (binary variable) and the detection of their localization (center of a component). The software was used to produce a submission to the MICCAI 2017 Endoscopic Vision SubChallenge.
Allows detection of cervical pre-cancers. This algorithm includes feature extraction and classification for acetic acid (VIA) and Lugol’s iodine (VILI) cervigrams. It can extract color and textural-based features. This algorithm performs by pre-processing images to reduce specular reflection, and automatically segmenting a region of interest from the cervix for analysis.
Performs a semantic segmentation of images. DeepLab is an extension of the Caffe software that is based on a combination of Deep Convolutional Neural Networks (DCNNs) and Conditional Random Field (CRFs) methods. The application is able to segment objects at multiple scales, to perform localization, generate semantic segmentation and recover objects boundaries.
Provides an approach for semantic segmentation of robotic instruments. This software utilizes several deep neural network architectures and avoids the binary segmentation that consists of the labeling of every pixel in an image as an instrument or background from the surgery video feed. This method has won the MICCAI 2017 Endoscopic Vision Sub Challenge: Robotic Instrument Segmentation.
Permits users to decompose an image into semantic regions. USEAQ is a superpixel extraction approach that performs joint spatial and visual quantization. This application uses the spatial and color quantization simultaneously to decompose an image. It (i) retrieves the grid, based on the positions of pixels, and preserves the spatial relationships between pixels and initial regions, and (ii) divides pixels into groups based on their colors.
Performs image segmentation and registration. CMP-BIA is dedicated to ImageJ/Fiji and contains a plugin named jSLIC. This plugin is a segmentation method for clustering, in a given image, similar regions (as known as superpixels) which are usually used for other segmentation techniques, classification and registration. It gives reliable superpixels shapes, with no need of decreasing their size.
Allows analysis the macroscopic structure of veins in leaves. LEAF GUI is a program built upon a series of algorithms designed to threshold, clean, and segment images of leaves in which the vein structure is visible. The software enables users to extract descriptive statistics on the dimensions and positions of leaf veins and the areoles they surround by following a series of thresholding, cleaning, and segmentation algorithms given images of leaves where veins have been enhanced relative to the background.
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