Center for Bio-Image Informatics

2009-10-01. New NSF Project on Mapping the Retina (2009-13)

The center faculty (Fisher, Manjunath, Rose and Singh), together with Robert Marc and Bryan Jones at the University of Utah, have received funding from the NSF to map the vertebrate retina. The project is titled "Computational Challenges in the Discovery and Understanding of Complex Biological Structures through Multimodal Imaging". The project start date is Oct 1, 2009 and is for four years.

NSF Link for the project

2009-08-01: NIH Project on Morphomic Analysis

Professors Smith and Manjunath have received a two year NIH award to carry out research on "Morphomic Analysis of a Simple Chordate." Organs and tissues are built during embryogenesis through the precise interactions of a myriad of cells and cell types. Advances in tissue repair and engineering will require that the rules and mechanisms that govern how cells come together to form organs and tissues be elucidated. This project will combine the efforts of developmental biologists and computer engineers to capture and analyze images from live embryos with the goal of understanding cell behaviors in forming organs.

Bisque - Bio-Image Semantic Query User Environment

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.

Bisque installer improvements

Bisque has an improved installer that makes bisque deployments much easier to manage. The installer is based on the python virtual environment shielding users from many system installation issues while making cross platform installation a breeze. Bisque is now easily installed on Linux, Windows and Mac OS platforms. More information is available at the Bisque Developer Site

Web Applications available in Bisque

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.

NSF Award on Uncertainty Management in Working with Scientific Images

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.

3D Retina visualization

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.

Scientist's Digital Notebook

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...