Bisque: a platform for bioimage analysis and management

Abstract

We present Bisque, a web-based platform specifically designed to provide researchers with organizational and quantitative analysis tools for 5D image data. Users can extend Bisque with both data model and analysis extensions in order to adapt the system to local needs. Bisque's extensibility stems from two core concepts: flexible metadata facility and an open web-based architecture. Together these empower researchers to create, develop and share novel bioimage analyses. Several case studies using Bisque with specific applications are presented as an indication of how users can expect to extend Bisque for their own purposes.

Advanced light microscopy core facilities: Balancing service, science and career

“…By designing workflow arrangements via an intuitive graphical user interface, both expert and non‐expert users gain access to automated image and data analysis solutions. The strength of such a platform or other tools like OMERO (Open Microcopy Environment Remote Objects, (Allan et al, 2012) [20]) and BISQUE (Bio‐Image Semantic Query User Environment, (Kvilekval et al, 2010) [21]) is that they are separated from the software pieces that actually do the work.…”

Communication Platform for Image Analysis and Sharing in Biology

“…1 (c) for a representative example of 3D volume rendering with curved surface image visualization by our system. In contrast to the specialized system, OMERO [2] and Bisque [35] are both web-based systems that focus mainly on data management for multidimensional images accessed and used via a web browser (OMERO also has its own client) on Mac, Windows, and Linux operating systems. Unfortunately, OMERO and Bisque are only equipped with simple image processing functions.…”

“…This system is designed only for non-interactive image processing and does not provide visualization functions. Although the pattern recognition methods implemented in [59] are powerful, such as a genetic algorithm and Support Vector Machine (SVM), and PSLID includes an image classification function, all the conventional cloud-based systems mentioned in this paragraph [2,35,45,59, 66] lack either 3D visualization or advanced 3D image processing abilities. In addition, it is difficult to incorporate conventional image processing tools [53,31,33] into these systems [2,35,45,59,66].…”

A GWAS platform built on iPlant cyber-infrastructure

“…The extended data store will also facilitate data transfer between iPlant and public data repository (e.g. pathway database), provide quality control (QC), support image based phenotyping [21,38], and enhance visualization.…”