Meets the growing need for a user-friendly, extensible, open-source solution for digital pathology and whole slide image analysis. QuPath provides researchers with powerful batch-processing and scripting functionality, and an extensible platform with which to develop and share new algorithms to analyze complex tissue images. It aims to help improve the speed, objectivity and reproducibility of digital pathology analysis and biomarker interpretation.
Handles large quantities of low contrast whole slides images using advanced cell detecting algorithms. The slideToolkit has been developed for modern personal computers and high-performance clusters. It provides a free, powerful and versatile collection of tools for automated feature analysis of whole slide images to create reproducible and meaningful phenotypic data sets. A workflow consists of four consecutive steps: (i) whole slide images are collected and converted to TIFF files; (ii) files are organized; (iii) creates multiple manageable tiles to count; (iv) tissue is analyzed and results are stored in a data set.
Assists in cell nuclei counting and staining estimation of accurate immunohistochemical (IHC)‑stained tissue slices and tissue microarrays (TMAs). TMARKER is a toolkit suitable for cancer cell nucleus setection, segmentation, counting, and classification (malignant/benign and stained/unstained). The software uses a superpixel‑based approach for classification. One of its advantages is the reproducibility of competitive cell counts.
It is the ideal "glue" for easily integrating dissimilar fluorescent microscope hardware and peripherals into a single custom workstation, while providing all the tools needed to perform meaningful analysis of acquired images. The software offers many user-friendly application modules for biology-specific analysis such as cell signaling, cell counting, and protein expression.
A tool for creating and analyzing realistic, meaningful, and quantifiable neuron reconstructions from microscope images. Perform detailed morphometric analysis of neurons, such as quantifying: 1) the number of dendrites, axons, nodes, synapses, and spines, 2) the length, width, and volume of dendrites and axons, 3) the area and volume of the soma and 4) the complexity and extension of neurons.
Supports the histopathological diagnostic workflow. Caseviewer is a viewer that works with whole slide images. As a digital microscope application, this method is also designed to handle the microscope examination process in bioscience. It provides several features (i) to count stained cells, immune-positive cell structures or count mitosis in the tissue or (ii) to optimize digital slides based on black, white and gamma values.
Measures the stain intensity of cell nuclei, cytoplasm, and membrane in parallel. CellQuant module assigns ’immunostain’ or ’counterstain’ to the different cell compartments. This module supports brightfield and fluorescent sample analysis. It can be easily calibrated to the automated immunohistochemistry (IHC) stain protocol of user’s laboratory by applying integrated color deconvolution to separate immunostain from counterstain.
Provides assistance for quantitative image analysis within cancer diagnostics. ONCOTOPIX intends to automate most of the daily routines of a pathologist’s work. It contains several software modules that covers multiple features such as visualization of scanned tissue slides or analysis of immunohistochemistry (IHC) and In-Situ Hybridization (ISH). This software is compatible with dedicated scanning hardware.
Allows researchers to conduct computer-assisted image investigation. QuantCenter is designed to quantify whole slide. It delivers a consistent standard to assist pathologists in diagnosis. This application was created for 3DHISTECH's image analysis. It provides a set of six different modules: patternquant module, histoquant module, nuclearquant module, membranequant module, cellquant module, and densitoquant module.
Performs automatic evaluation on immunohistochemistry (IHC) nuclear stainings. NuclearQuant detects cell nuclei and measures staining intensity on the chromogen channel using color deconvolution. This method categorizes the detected nuclei to negative, weak positive, medium positive and strong positive classes. This software has an In-Vitro Diagnostic (IVD) certification for Estrogen (ER) and Progesterone (PR) quantification.
Detects the basic components in an Immunohistochemistry (IHC) image. IHC Toolbox was developed using a semi-automatic scheme that is suitable for different kinds of IHC image analysis. The software includes functions for semi-automatic color selection, automatic statistical color detection, automatic nuclei segmentation and automatic gland detection. It allows users to save and transfer their created models and parameters to different users for the reproduction of detection results in different laboratories.
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