Center for Bio-Image Informatics

Engineering, Biology and Computer Science, working together.

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BisQue 0.5.6 release

BisQue 0.5.6 released on October 13, 2014!

We are very pleased to announce a new release of the BisQue system: 0.5.6. This release introduces a big update in the underlying system to support resource (images, packages, videos) composed of many files. This improvement allows BisQue to operate on images composed on many files in place, with no additional re-conversions. We can now support Tiff-Series and proprietary formats like Volocity and AndorIQ in-place. Insertion of such images has become much faster since we don't do any special processing on ingest. As usual we have some UI improvements and great new productivity features.


CellECT: Cell Evolution Capturing Tool

Introducing CellECT Software for Interactive Segmentation of 5D Datasets

We introduce CellECT Cell Evolution Capturing Tool, a software package for the interactive segmentation and analysis of 3D+t microscopy volumes. CellECT enables users to interactively segment microscopy time series of volumes of membrane (and nuclei) channel datasets. The software includes an adaptive cellness metric which highlights regions of uncertainty in the segmentation. This metric learns from the user feedback and from each specific dataset and guides the user towards problematic regions. Additionally, CellECT provides an analysis module which computes shape analysis statistics over time and clusters similar cells into tissues. CellECT can import nuclei detected with a of a nuclei detection algorithm such as such as (Fick, 2013) available on the Bisque bio-image analysis platform. CellECT main window

Full control of the directory tree

BisQue users can now control the cloud-based file storage to the level of directories. Resources are now organizable not only by Bisque annotations but also by the directory structure. This allows keeping exactly the same structure as on one's hard-drive. Uploading and downloading these structures is super easy and is fully supported in the Chrome browser. Users can now drag and drop directories directly into upload page, wrap all the files into a dataset and analyze it with a few clicks.


BisQue offers openslide support

Openslide allows reading whole-slide (very large planar) images in various formats: Aperio, Hamamatsu, Leica, MIRAX, Sakura, Trestle and generic tiled and pyramidal TIFF. Openslide's efficient library enables BisQue to read pixel data on demand and cache extracted tiles for better performance in the future. This translates into seamless visualization, annotation and analysis of images in all of the above formats. As usual all annotations are stored in the BisQue database and are not modifying the original files thus making BisQue a perfect tool for medical image analysis.

View the 95Kx67K sample image

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.


iPlant Collaborative offers BisQue for plant biologists

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.

BisQue 0.5.5 released on May 9, 2014!

We are very pleased to announce an exciting new release of the BisQue system: 0.5.5. There are many new features, improvements and fixes for everybody from end-users to administrators.


  1. Directory Support and Import/Export
    1. Directory import and export (drag and drop directories with sub directories)
    2. Tree view of directories in the system
    3. New BisQue archives with support for all resources
  2. Many new image formats: ImarisConvert, OpenSlide and BioFormats 5 add more than 100+ new and well supported image formats
  3. New share and dataset functionality
    1. New share dialog
    2. Dataset view highly improved making all operations dataset-wide
  4. Image viewer improvements
    1. Image view - graphical annotations editing, saving/loading, pixel counting UI
    2. Movie view - new html5 image as movie view

The BisQue team has made a change in the license. The change requires proper and visible attribution of our project if the whole or parts of the BisQue system are used for either research or commercial purposes. Please, refer to the new license for more details.

Image measurements in the web browser

The new BisQue web interface enables various image measurements directly in the browser. It's easy to measure length and area of any graphical object in pixels and physical units by simply drawing objects of interest and all the measurements will be displayed promptly in the viewer window. Moreover, BisQue enables rapid area estimation for any number of objects based on thresholding and segmentation. By using a Pixel Counter tool (found in Operations -> Pixel Counter) users can select a threshold value and click on objects of interest in order to segment them and append their area into the measurements list.

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.


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"



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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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.

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