Data management/Annotation software tools | Bioimaging
Advances in the field of microscopy have brought about the need for better image management and analysis solutions. Novel imaging techniques have created vast stores of images and metadata that are difficult to organize, search, process and analyze.
A software platform that enables access to and use of a wide range of biological data. OMERO uses a server-based middleware application to provide a unified interface for images, matrices and tables. OMERO's design and flexibility have enabled its use for light-microscopy, high-content-screening, electron-microscopy and even non-image-genotype data.
Allows researchers to manage health and medical research data for humans and animals without specialized database skills or programming expertise. The Ark provides data management for core research information including demographic, phenotype, biospecimen and pedigree data, in addition to supporting typical investigator requirements such as tracking participant consent and correspondence, whilst also being able to generate custom data exports and reports. The Ark is study generic by design and highly configurable via its web interface, allowing researchers to tailor the system to the specific data management requirements of their study.
A software package for running highly comparative time-series analysis. hctsa automates the selection of quantitative phenotypes from time-series data by leveraging a large and interdisciplinary literature on time-series analysis. hctsa allows thousands of time-series analysis features to be extracted from time series (or a time-series dataset), as well as tools for normalizing and clustering the data, producing low-dimensional representations of the data, identifying discriminating features between different classes of time series, learning multivariate classification models using large sets of time-series features, finding nearest matches to a time series of interest, and a range of other visualization and analysis functionality.
Helps expedite and facilitate the transformation of raw phenomic character data into discrete character matrices that can be used in most popular evolutionary inference programs. MatrixConverter facilitates the process of evaluating, scoring, and formatting raw phenomic data so that the data can be used for evolutionary inference.
Enables visualization, storage and sharing of large image data. Biolucida is data management, analysis and visualization system, and a hub for users 2D and 3D image such as 2D/3D slide scanners, confocal Z-stacks and lightsheet whole brain images. Data is stored in a secure and permanent way. The software can be useful for research, medical education, and for publishers. A free application named ‘Biolucida Viewer’, for viewing public images or images shared by collaborators owning Biolucida, is also available.
Allows users to manage statistically processed data. Genotype Viewer generates organized web content and provides genotype-oriented summaries across mutant strains or cohorts. It is a part of the Phono-pub platform that integrates workflows for three types of data handling that support the steps from data analysis to publication of mouse phenotypic data obtained in a variety of analyses. Genotype Viewer can serve in phenotyping experiments.
Offers well-established, broadly validated measures of phenotypes and exposures relevant to investigators in human genomics, epidemiology, and biomedical research. PhenX Toolkit is a catalog of recommended, standard measures of phenotypes and environmental exposures for use in biomedical research. It provides detailed protocols, information about the measures, and tools to help investigators incorporate PhenX measures into their studies.