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TMA Navigator
An open access web application for analysis of TMA data and related information, accommodating categorical, semi-continuous and continuous expression scores. Non-biological variation, or batch effects, can hinder data analysis and may be mitigated using the ComBat algorithm, which is incorporated with enhancements for automated application to TMA data. Unsupervised grouping of samples (patients) is provided according to Gaussian mixture modelling of marker scores, with cardinality selected by Bayesian information criterion regularization. Kaplan-Meier survival analysis is available, including comparison of groups identified by mixture modelling using the Mantel-Cox log-rank test. TMA Navigator also supports network inference approaches useful for TMA datasets, which often constitute comparatively few markers. Private anonymous access is available, and user accounts may be generated for easier data management. An extensive user guide and demonstration datasets are available.
cancergrid-tma
An open source web-based application for remote scoring of tissue microarray (TMA) images, which exploits the value of Microsoft Silverlight Deep Zoom to provide an intuitive interface for zooming and panning around digital images. We use and extend existing XML-based standards to ensure that the data collected can be archived and that our system is interoperable with other standards-compliant systems. cancergrid-tma has been used to automate a workflow for the high-throughput manual scoring of thousands of TMA images and make the results available for integration with clinical data.
ImageMiner
Provides users to perform high-throughput comparative analysis and reproducible characterization of expression profiles in imaged tissue microarrays (TMAs). ImageMiner applies cascades of computerized image-processing methods on multiple arrays. It segments each disc image into spatial structures, computes a set of features for each segmented structure, and classifies the disc images on the basis of the resulting feature signature. This tool reduces the obstacles of conducting collaborative research projects.
HiPath
Determines programmed death-ligand 1 (PD-L1) protein expression by calculating the percentage of viable tumor cells showing partial or complete membrane staining. HiPath is a highly intelligent computerized scoring aid for quantitative immunohistochemistry and chromogenic in situ hybridization (CISH) assays. This software helps in review and analysis of tissue samples and helps a pathologist reach the possible diagnostic conclusions by providing automated counting and statistical analysis of all cells within a region of interest, as well as across multiple regions of view.
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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