Center for Bio-Image Informatics

Engineering, Biology and Computer Science, working together.

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Bisque 0.5.4 is out!

The latest Bisque release offers faster speeds and many new and exciting features:

  • Improved login architecture
  • Faster and much enhanced image service
  • New image operations: pixel counter, rearrange dimensions, thresholding, gamma, 3D interpolation, superpixels segmentation, flip mirror and rotation guessing based on EXIF, image transforms space: fourier, wavelet, chebyshev, etc. color: HSV, etc,), filters (edges, colors)
  • New feature service to compute image and graphical object feature descriptors supporting more than 100 descriptors
  • Many UI improvements: complex image annotations, better toolbar
  • Nuclear Detector is 100X faster, fully CPU parallelized and uses GPU if available
  • Nuclear Detector now supports any 4D image sizes (processed 26GB image in 2h)
  • New Nuclear Filtering module for brightfield 3D images
  • Read more about the Bisque system.


    Bisque for plant biologists (iPlant)

    Bisque is now available at iPlant for plant biology researchers. iPlant is a community of researchers, educators, and students working to enrich all plant sciences through the development of cyberinfrastructure. Interested plant researchers can gain access to extensive hardware and software resources, including the Bisque imaging and analysis platform. Read more about Bisque on iPlant.

    Pfizer labs use BISQUE

    The bio-image analysis platform, Bisque, developed at the Center for Bio-Image Informatics at UCSB, will be used for data sharing and analysis at the Pfizer Neuroscience Research Unit (NSRU). The Bisque software platform offers several unique functionalities for large scale data management, including an advanced software architecture based on state of the art web protocols, advanced large scale data visualization, tight integration of image analysis with database services, and scalable computing using cloud computing. The NSRU optical Imaging lab, led by Joel Schwartz, is developing quantitative methods that process the images, keeping track of the processing workflow, and allowing scientists to create new work flows that seamlessly combine multimodal data.


    Center for Bio-Image Informatics works with Marine Science Institute at UCSB, NOAA and Greenpeace to analyze large collection of underwater videos

    A collaborative project between Center for Bio-Image Informatics, Marine Science Institute at UCSB, NOAA and Greenpeace has acquired and analyzed 23 hours of HD underwater video by identifying all species present in the videos and producing co-occurrence statistics. A complete dataset of annotated sampled frames is published by the Center on our Bisque server. A paper have been published in PLoS ONE about this effort: "Structure-Forming Corals and Sponges and Their Use as Fish Habitat in Bering Sea Submarine Canyons"

    Media reaction

    Washington Post reports about this project: "Fishery managers could call for a review of massive underwater canyons"

    Mission blue writes: "Canyons in the Deep"

    UCSB Press release: "UCSB Teams With Greenpeace and NOAA to Study World's Largest Undersea Canyons"


    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.


    Christopher Goldsmith wins award for his 2011 summer internship work

    Christopher Goldsmith recently received an award for his poster at The Emerging Researchers National (ERN) Conference in Science, Technology, Engineering and Mathematics (STEM). The poster presented work done during his 2011 summer internship during which he worked under Carter De Leo on evaluation of video summarization algorithms. More detail on his project can be found here. The ERN Conference is hosted by the American Association for the Advancement of Science (AAAS), Education and Human Resources Programs (EHR) and the National Science Foundation (NSF) Division of Human Resource Development (HRD), within the Directorate for Education and Human Resources (EHR). It is aimed at college and university undergraduate and graduate students who participate in programs funded by the NSF HRD Unit, including underrepresented minorities and persons with disabilities. He received 2nd place in the Poster Presentations in the category of Computer Sciences and Information Systems and Computer Engineering. More information on the award can be found here.

    Christopher also went on to receive an LSAMP-BD fellowship (fellowship info)  from the NSF which entails completion of a master's degree at CSULA in 2 years with fully paid tuition and a $30,000 yearly salary and application to PhD. programs in the fall of 2013 with the intentions of starting a program in the fall of 2014. Congratulations Christopher!


    4D image visualization

    New "BioView3D" visualizes 3D/4D/5D images.

    * Visualization video of the laser scanning confocal image of cell mitosis stages Metaphase-Anaphase by fluorescent tagging of mitotic spindles, courtesy of Alphan Altinok, Caltech.


    2013 Summer Internship

    From June through August 2013, we hosted summer interns from Dos Pueblos High School, Cal-State San Bernadino, Brown University and UCSB. To find out more about our students and their projects, read more below.



    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.
    Read More

    Research Programmer  Position Available  

    Requirements:  Database and Web experience required (i.e.  Turbogears, RubyOnRails, etc).  Projects in many areas including semantic web integration, image-content and geometrical searching. Experience with python, javascript, CSS, HTML required.

    Full Descrption

    Online Databases