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.
Performs automated microglia morphology analysis from whole slide imaging (WSI). Microglia Analysis is an automated end-to-end system that assesses microglial activation in white matter regions on whole slide images of Iba1 stained sections. The software takes an Iba1-stained brain slide consisting of several coronal cross sections, segments the white matter regions, and identifies all microglial cells in these white matter regions to yield analyses of both cell count and morphology. It can increase standardized analysis of brain slides.
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.
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