BisQue

BisQue[1] is an open source web-based platform for the exchange and exploration of large, complex datasets being developed and supported by ViQi. BisQue specifically supports large scale, multi-dimensional multimodal-images and image analysis. Metadata is stored as arbitrarily nested and linked tag/value pairs, allowing for domain-specific data organization. Image analysis modules can be added to perform complex analysis tasks on compute clusters. Analysis results are stored within the database for further querying and processing. The data and analysis provenance is maintained for reproducibility of results. BisQue can be deployed in cloud computing environments or on computer clusters for scalability. BisQue has been integrated into the NSF Cyberinfrastructure project CyVerse.[3] The user interacts with BisQue via any modern web browser

Some key ingredients are:

• Flexible schema for scientific data management

• Integrated analysis system

• Search by content and metadata

• Data visualization system

Some current user of BisQue are:

• Cyverse.org

• Allen Cell Institute

History

The BisQue project originated at the University of California, Santa Barbara in 2008

Project BisQue originally started in 2004 as part of the US National Science Foundation (NSF) supported Center for Bio-Image Informatics at UCSB, to facilitate integration of database and image analysis methods, specifically in the context of microscopy images. Given the diversity of imaging equipment and image formats, there was an urgent need to access multiple formats in a uniform way. More importantly, there was also a need for maintaining the analysis provenance for reproducing image analysis results. Very early on, it was realized that BisQue has to go schema-less to support the needs of diverse biological experiments—each experiment and analysis results are unique and slightly different. Further, from the beginning, BisQue focused on using the web browser as the standard interface. These posed unique database and visualization challenges while dealing with large scale multimodal data, and in the process BisQue has developed a unique and novel framework for visualizing very large images (100k x 100k pixels, for example), and currently supports over 250 different image file formats. Within the browser, users can now visualize 2D, 3D, 4D and 5D images, and export them to many other standardized formats. Over the years the BisQue team has closely worked with the iPlant Cyberinfrastructure (now the CyVerse), supporting the image database management needs of the plant biology community.

Going beyond Bioimaging applications, BisQue has been used in analyzing underwater images and video (REF here) and in medical imaging applications. The current BisQue interface now supports the latest DICOM standard. BisQue has integrated over 100 different image features in its feature service and the next release will include support for deep learning methods and feature classification services.

Licensing

Open Source BisQue was fully Licensed from the University of California in 2017. Current version of Open-Source Bisque are available under a Dual-License (AGPL or Commercial). Versions before 0.5.10 have BSD licence.