Center for Bio-Image Informatics

Engineering, Biology and Computer Science, working together.

 
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UCSB Bio-Segmentation Benchmarking

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The UCSB Bio-Segmentation Benchmark dataset consists of 2D/3D images and time-lapse sequences that can be used for evaluating the performance of novel state of the art computer vision algorithms. Tasks include segmentation, classification and tracking. For each class of problem, at least one ground truth dataset is available. We also provide performance metrics for comparing the results of the algorithms with the ground truth. Additional ground truth data will be posted as they become available.

 

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Web Applications available in Bisque

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We have started beta-testing for a first set of web applications. These applications do not require local install and use the CPU time of our servers. The web application incapsulates the entire analysis module workflow with specifically designed user interface. Currently we provide 3D Nuclei Detection and Microtubule tracking applications.
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New $3 Million NSF Award on Uncertainty Management in Working with Scientific Images

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The Center for Bio-Image Informatics faculty have been awarded a new 5 year NSF project that would explore new, fundamental problems in uncertainty analysis while working with image data. The principal investigators on the project include Professors Hollerer, Manjunath, Rose and Singh on the Engineering side and Professors Feinstein, Fisher and Wilson from the biology division.

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2008-01-18 Workshop on Bio-Image Informatics

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Workshop on BioImage Informatics at UCSB

Our recent Workshop on "Bio-Image Informatics: Biological Imaging, Computer Vision and Data Mining" was a great success with over 150 attendees from bioimaging and related fields.

UCSB, Santa Barbara, CA, USA, January 17-18, 2008.

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Bisque - Bio-Image Semantic Query User Environment

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Bisque (Bio-Image Semantic Query User Environment) 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.

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Presentation slides (pdf format)

 

 

Scientist's Digital Notebook

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 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. More info...

 

3D Retina visualization

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Open source and cross platform software "BioView3D" to visualize confocal laser scanning images on common OpenGL enabled hardware and provide competition to expensive proprietary alternatives.

* Visualization video of the laser scanning confocal image of cat retina stained with PKC and VAMP.

 

Highlights

Bisque System

Bisque provides flexible image and metadata organization, database aggregation and distribution, and an extended image analysis architecture. The system has incorporated research in many areas including: biological image processing, novel distance measures, index structures, search algorithms, and data mining techniques.
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Programmer  Position Available  

Requirements:  Web page contruction and experience with web application frameworks required (i.e.  Turbogears, RubyOnRails, etc).  Experience with python, javascript, CSS, HTML required.

Full Descrption

Online Databases

BISQUE