Abstract
Image acquisition, processing, and quantification of objects (morphometry) require the integration of data inputs and outputs originating from heterogeneous sources. Management of the data exchange along this workflow in a systematic manner poses several challenges, notably the description of the heterogeneous meta-data and the interoperability between the software used. The use of integrated software solutions for morphometry and management of imaging data in combination with ontologies can reduce meta-data loss and greatly facilitate subsequent data analysis. This paper presents an integrated information system, called LabIS. The system has the objectives to automate (i) the process of storage, annotation, and querying of image measurements and (ii) to provide means for data sharing with third party applications consuming measurement data using open standard communication protocols. LabIS implements 3-tier architecture with a relational database back-end and an application logic middle tier realizing web-based user interface for reporting and annotation and a web-service communication layer. The image processing and morphometry functionality is backed by interoperability with ImageJ, a public domain image processing software, via integrated clients. Instrumental for the latter feat was the construction of a data ontology representing the common measurement data model. LabIS supports user profiling and can store arbitrary types of measurements, regions of interest, calibrations, and ImageJ settings. Interpretation of the stored measurements is facilitated by atlas mapping and ontology-based markup. The system can be used as an experimental workflow management tool allowing for description and reporting of the performed experiments. LabIS can be also used as a measurements repository that can be transparently accessed by computational environments, such as Matlab. Finally, the system can be used as a data sharing tool.
Highlights
Processing and extraction of information from images have become indispensable aspects of the experimental workflow in life science research, and in particular in cell biology and neuroscience (Swedlow and Eliceiri, 2009)
This paper presents an integrated information system, called LabIS
The user interface (UI) of LabIS is divided in 5 main modules: Project planning, Subject management, Manipulation management, Image Measurements and Morphometry, and System Administration
Summary
Processing and extraction of information from images have become indispensable aspects of the experimental workflow in life science research, and in particular in cell biology and neuroscience (Swedlow and Eliceiri, 2009). According to the estimates of Swedlow and Eliceiri (2009) there are approximately 80 proprietary file formats for optical microscopy alone that must be supported by any imaging tool for life science microscopy which aims to provide a general purpose solution This lack of standardization of the meta-data has been recognized as a hindrance for the microscopic field (Goldberg et al, 2005; Linkert et al, 2010). Measurements can not be regarded as image “features.” This consideration introduces a distinction between “image-centric” and “process-centric” approaches in management of experimental information An example of the former approach is the web application Open Microscopy Environment (OME; Goldberg et al, 2005). At the time of writing there were 81 such ontologies present at the OLS hub and more than 200 in the BioPortal site
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