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Cytomine
An open-source, rich web environment to enable highly collaborative analysis of multi-gigapixel imaging data. Cytomine (i) provides remote and collaborative principles, (ii) relies on data models that allow to easily organize and semantically annotate imaging datasets in a standardized way, (iii) efficiently supports high-resolution multi-gigapixel images, (iv) provides mechanisms to readily proofread and share image quantifications produced by machine learning-based image recognition algorithms.
VirtualMicroscopy
A real time virtual microscopy technique for interactive analysis of super high resolution microscopic images over internet on standard desktops, laptops or mobile devices. VirtualMicroscopy technique is demonstrated to perform as fast as using a microscopy locally without any delay to assess gigapixel ultra high resolution image data through wired or wireless internet by a Tablet or a standard PC. More importantly, VirtualMicroscopy enables analysis of super high resolution microscopic image across sites and time and allows multi-person analysis at the same time, which greatly speed up data analysis process and reduces miscommunication among scientists and doctors.
slideToolkit
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.
GRAPHIE / GRAPh based Histology Image Explorer
Allows users to explore, annotate and discover potential relationships in histology image collections. GRAPHIE is a visual analytics tool designed to assist pathologists and systems biology researchers It discovers, annotates and reveals potential relationships of phenotypical properties within a biologically relevant context. This tool uses the bag-of-features (BoFs) approach to capture visual patterns from a given collection of histology images, and thus allowing a semantic organization of unstructured image collections.
Pannoramic Viewer
Enables users to view the sample. Pannoramic Viewer is a digital microscope application that permits to make annotations and measurements. These functions can be easily expanded through its various software modules. It provides several features: (i) Seamless zooming and moving of the virtual slide, (ii) bookmarking on the spot, defining the specific part of the sample by drawing, finding and reading of previously made bookmarks, or (iii) fluorescent slide handling, separate channel view & pseudo-colorization.
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