BisQue (Bioimage Analysis and Management Platform)
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| Developer(s) | University of California, Santa Barbara |
|---|---|
| Stable release | 0.5.8
/ October 1, 2015 |
| Written in | Python |
| Operating system | Linux, OS X, Windows |
| Available in | English |
| Type | Image analysis / Data Mining / Data Analysis |
| License | FreeBSD license |
| Website | bioimage |
BisQue[1] is a free, open source web-based platform for the exchange and exploration of biological images. It is being developed at the University of California, Santa Barbara. The BisQue system is centered around a database of images and metadata and supports the entire workflow from image capture to image analysis and querying. 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. The user interacts with BisQue via any modern web browser.
History
To be added.
This is a test
Features
BisQue provides an online resource for management and analysis of 5D biological images. In addition to image collection management, the system facilitates common biological workflows typical of biological images: imaging, experimental annotation, repeated analysis and presentation of images and results.
Ingestion of images and metadata
Image and metadata ingestion is the first step in using BisQue. The ingestion can either happen through a web browser-based interface, or via the BisQue API. To date, BisQue supports over 240 different image formats[2] from generic Jpeg to specialized microscopy image formats such as Zeiss CZI, Imaris Ims, and Nikon ND2.
Images can be arbitrarily large and are automatically pyramided after ingestion. This guarantees a fluent user experience when panning and zooming in the image viewer.
Annotation with textual and graphical metadata
Images and metadata are organized with tags (name–value pairs) associated with an image.[1] BisQue allows an arbitrary number of tags per resource and arbitrary nesting between tags, similar to XML documents. This provides a very flexible way of managing information, tailored to the needs of the underlying imaging project. For efficiency and reliability, the tags and values are stored in an indexed tag/value table in the underlying SQL database.
Graphical annotations can be stored in addition to tags. They include simple objects such as points, lines, and circles, and more complex objects such as region outlines. In addition to be searchable, these graphical annotation are also rendered in BisQue's image viewer as overlays on top of the viewed image.
Organization and search
Users typically locate images of interest by browsing through collections or by searching with specific queries. For the former, BisQue provides a web-based tag organizer that enables rapid filtering and grouping of large image collections by tag names and values. For the latter, BisQue offers a RESTful tag query interface to find images with specific tag values. Both of these search capabilities are converted into SQL queries over the tag/value table behind the scenes.
ADD FEATURE SERVICE!!!
Parallel analysis modules
REWRITE THIS (modules, condor)!!!
BisQue provides an extensible analysis system that allows both internal and external analysis and visualization tools. Internal analysis methods are executable through the web, providing ease of use while transferring the computation load to the BisQue servers. Furthermore, BisQue facilitates "web applications", custom user interfaces built around an analysis problem and its results encapsulating a predefined workflow. An external analysis refers to a tool remotely accessing data within the BisQue system that may utilize special hardware or other local features not available through the web. External tools are also useful for rapid prototyping of analysis before creating an internal version. Results produced by either internal or external tools may be stored back into the system in the form of tags, graphical objects and/or images.[1]
Visualization and sharing
Metadata in BisQue can take many forms: text, objects of interest, user annotations or another web-based file (e.g. associated publication in PDF). Textual and graphical markup viewing and editing is available in the web 5D image viewer. The viewer is used for image and object browsing, ground-truth acquisition and statistical summaries of biological objects. Additionally, it allows for various visualization options such as channel mapping, image enhancement, projections and rotations.[1] The most recent image viewer is able to present volumetric imagery in 3D without browser plug-ins by utilizing modern browsers' WebGL capabilities.[2]
Biological image sharing has often been difficult [3] due to proprietary formats. In BisQue, sharing images, metadata and analysis results can be performed through the web. The system contains an export facility that allows conversions of image formats, application of a variety of image-processing operations and export of textual or graphical annotations as XML, CSV or to Google Docs.
RESTful interface
All services and modules are accessible via standard web access methods (HTTP). This permits a wide variety of tools, from web browsers to custom analysis applications, to interact with BisQue. Most BisQue services are implemented using the RESTful design pattern architecture that exposes resources through URIs. Resources are manipulated by using the common HTTP methods. Among many benefits attributed to RESTful pattern are scalability through web caches and the use of client side state and processing resources.[4] Bisque services exchange data in XML format.
For easy integration with existing software, BisQue also provides an API that covers all aspects of resource ingestion, search, analysis, and manipulation. It is currently available for Python and Matlab.
License
As of version 0.5.5, BisQue is released under a modified BSD license that requires proper and visible attribution of the BisQue project if the whole or parts of BisQue are used for either research or commercial purposes.[5]
References
- ^ a b c d Kvilekval, Kristian; Fedorov, Dmitry; Obara, Boguslaw; Singh, Ambuj; Manjunath, B.S. (2010). "Bisque: A Platform for Bioimage Analysis and Management". Bioinformatics. 26 (4): 544–552.
- ^ a b BisQue website, retrieved 11/02/2015.
- ^ Andrews, P.D.; Harper, I.S.; Swedlow, J.R. (2002). "To 5D and beyond: quantitative fluorescence microscopy in the postgenomic era". Traffic. 3 (1): 29–36.
- ^ Fielding, R.T.; Taylor, R.N. (2002). "Principled design of the modern web architecture". ACM Trans. Internet Technol.: 115–150.
- ^ BisQue license