Bisque (Bio-Image Semantic Query User Environment) : Store, visualize, organize and analyze images in the cloud. Bisque was developed for the exchange and exploration of biological images. The Bisque system supports several areas useful for imaging researchers from image capture to image analsysis and querying. The bisque system is centered around a database of images and metadata. Search and comparison of datasets by image data and content is supported. Novel semantic analyses are integrated into the system allowing high level semantic queries and comparison of image content.
Features
- Bisque is free and open-source
- Flexible textual and graphical annotations
- Cloud scalability: PBs of images, millions of annotations
- Distributed storage: local, iRODS, S3
- Integrated image analysis, high-throughput with Condor
- Analysis in MATLAB, Python, Java+ImageJ
- 100+ biological image formats
- Very large 5D images (100+ GB)
Demos
Contact
- Please use the bisque-bioimage google group, you can e-mail us directly to This e-mail address is being protected from spambots. You need JavaScript enabled to view it .
Documentation
- Start with our paper for an overview and ideas behind the system.
- Presentation slides (pdf format)
- Project Wiki
- Create ticket (bug-reports/enhancements)
Source code
- Project Wiki (Trac timeline/tickets, Mercurial source code repository)
- Browse source on-line
MtQAT is a microtubule tracking and quantitative analysis software tool. MtQAT is in development for the analysis of microtubule dynamic instability. 
Documentation
BQBisqueJ is an ImageJ plugin that allows direct access to the Bisque DataBase system. 
iWall is a 20 monitor tiled display for viewing high resolution biological images. Advances in microscopy imaging and automatic image mosaicking are providing biologists with images of such resolution that they can't be properly viewed on standard displays. The UCSB iWall provides a 8000x 4800 pixel display (38.4 Megapixels) for viewing every detail of even the largest image 
BQJavaLib is a Java library for Matlab that allows direct access to the Bisque DataBase system. 
This application is designed to simplify the image annotation process. It allows researchers to create meta-data required by the bio-image database. It can also update, print and upload existing information. 
ITCN (Image-based Tool for Counting Nuclei) is an 
3D Nuclei Detector Matlab Toolbox allows you to automatically identify nuclei centroid locations on 3D confocal microscopic images. Furthermore these locations can be used for posterior analysis
such as nuclei outline segmentation or membrane segmentation.
BQC++Toolbox allows direct access to the Bisque DataBase system for C++ applications using Trolltech Qt library. 
This application is a command line image conversion utility. It can read and write many image formats, extract ROI and meta-data stored in images. Accepted image formats are: BioRad PIC, TIFF, OME-TIFF, Metamorph STK (uncompressed and LZW compressed), Fluoview, Olympus Image Binary (OIB), Carl Zeiss LSM 5, PSIA TIFF, Nanoscope II/III, JPEG, PNG, BMP, IBW, OME, RAW and video: QuickTime, AVI, MPEG1/2/4, Flash, etc.
bioView is an open source and cross-platform application intended for biologists to visualize EM, Confocal, etc. imagery. It runs on Windows, MacOS X and Linux. It also provides access from the remote controller that simplifies usage of the very large screens e.g. 8000x4800 pixels composed by many monitorsa and is used on iWall.
