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.
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.
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.
Offers an automatic tissue microarray (TMA) tool for brightfield and fluorescent images. ATMAD is based on a two-step method: it first identifies the core positions on the input TMA image and then segments them to reduce the number of false alarms. This software process by estimating the deformation of the design grid to compute the row and column coordinates of each localized tissue core.
Allows users to manage core sections under standard conditions. PATMA includes features for detecting not only cores but also “holes” places where the core should be located. This software performs with tissue microarrays (TMA) and scanned image. Moreover, it can assign successive numerical labels to all locations of designed array structure of the TMA.
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.
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.
Analyzes the cooperative behavior of all measured markers in a multifactorial tissue microarray (TMA) approach. The TMAinspiration method is specifically focusing on the demands of the TMA analysis by controlling errors and noise by a generalized regression scheme while at the same time avoiding to introduce a priori too many constraints into the analysis of the data.
Provides image analysis tools for segmentation, classification, and downstream analysis of tumour section images. CRImage is a Bioconductor package that allows cellularity scoring of tumours which can then be applied to correct molecular assay data for varying cellularity. It also comes with an algorithm for copy-number data correction given single nucleotide polymorphism (SNP) microarray data and cellular content of the tumours estimated by the image analysis.
Allows users to create a database for archiving, reviewing and processing images and data generated during analysis of your tissue arrays. TISALYS handles large volume of tissue array data and enables users to import tissue arrays slides analysis manually performed. Users can store their data, such as spot images, tissue microarray (TMA) slide previews, patient/animal data, experimental data, on the generated database. Data from commercial TMA slides and locally produced TMA can also be processed.
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.
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.
Assists in detection of viral RNA. CISHQuant module provides application with two different algorithms, CISH and CISH-RNA to the chromogenic in situ hybridization patterns. It offers features as (i) the reliable digital image processing on tissue samples for maximum support to pathologists, with rapid evaluation algorithm, (ii) the Measurement mode for mapping even widely separated cells or (iii) an user-friendly, transparent results display in a unique cell Gallery.
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.
Assists in designing tissue arrays from recipient block and tissue array map definition through to populating the map with chosen specimens. TMADesigner2 is a program that handles various punch size from 0,6 mm up to 4 mm. Users can adjust the density of cores, control and orientation cores, and grid organization.
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.
Serves as a tissue arrays analyzer tool. Spot Browser allows the exploration and analysis of tissue arrays captured in all light conditions: brightfield, darkfield, fluorescence and fluorescence in situ hybridization (FISH). This software includes an image database that enable the archiving of images, virtual slides, patient data/animal and experimental data. One of the main features of this tool is the possibility to score tissue arrays and to create different fields of annotations.
A statistical tool designed to support information and images related to tissue micro-arrays. TMAJ contains support for multiple organ systems, multiple users, image analysis, and is designed to be compliant with HIPPA regulations. It permits designing TMAs, viewing and scoring TMA images online, side-by-side viewing of serial TMA images from slides stained for different biomarkers, publishing large numbers of TMA images and datasets on the Internet.
Consists of a web-based application to collect all data required for tissue microarrays (TMA) studies (patient and tumor data, or block array information, array slide staining). TMABoost is a program able to capture an overview of the glass TMA slide as well as capturing high resolution images of each individual tissue core. These images are stored in the database and can be visualized by pathologists through the web interface. Moreover, automatic quantification of biomarker expression can be computed on these digital images.