Center for Bio-Image Informatics

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Center for Bio-Image Informatics / Downloads


Bisque Database

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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

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Documentation

Source code

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Microtubule Quantitative Analysis Tool

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MtQAT is a microtubule tracking and quantitative analysis software tool. MtQAT is in development for the analysis of microtubule dynamic instability.

Features

  • Automated or assisted microtubule tracking
  • Interactive graphical user interface
  • Integrated quantitative analysis of microtubule tracks
  • New statistical descriptors derived from the microtubule body

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Documentation

 

BQBisqueJ

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BQBisqueJ is an ImageJ plugin that allows direct access to the Bisque DataBase system.

Downloads

Requirements

Installation

BQBisqueJ requires adding a Bisque JAR file to ImageJ. In ImageJ 1.31 or later, this is done by copying the Bisque JAR file into the plugins folder or an immediate subfolder of the plugins folder, then restarting ImageJ.

  • OS X: To compile a plugin that uses a JAR file, copy the JAR file to /Library/Java/Extensions.
  • Windows: To compile a plugin that uses a JAR file, copy the Bisque JAR file to the Java extensions folder, ImageJ\jre\lib\ext.
  • Linux: To compile a plugin that uses a JAR file, copy the Bisque JAR file into the plugins folder.

Source code

 

iWall

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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

Features

  • Low cost - Open source multi-monitor image viewer
  • Easy control using remote client

Source code

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BQJavaLib

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BQJavaLib is a Java library for Matlab that allows direct access to the Bisque DataBase system.

Requirements

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Source code

 

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.

Features

  • User-defined meta-data annotations
  • Powerful graphical annotations with user-defined types
  • Bio-formats meta-data and file name parsing
  • Rapid upload for Bisque database
  • In-place simple statistics for graphical annotations

Downloads

Please, refer to our paper if you use this software.

Documentation

Source code

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Automatic Nuclei Counter plug-in for ImageJ

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ITCN (Image-based Tool for Counting Nuclei) is an ImageJ plugin for counting the number cells within an image. The inputs are: (1) an estimation of the diameter of a cell, (2) an estimation of the minimum distance between cells, and (3) either a region of interest (ROI) selected with ImageJ's selection tools or a black and white mask image that is white in regions that are to be counted. Already more than 1,000 downloads!

Features

  • Robust automatic nuclei detector
  • Integrates with popular ImageJ software
  • Tested on large variety of biological date, such as: confocal, light, etc.

Required Downloads

Documentation

Read more for Installation and configuration guide
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BQMatlabToolbox

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BQMatlabToolbox allows direct access to the Bisque DataBase system.

Requirements

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Source code

 

3D Nuclei Detector Matlab Toolbox

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Detected centroid positions of the nucleus3D 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.

Features

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Documentation

  • Coming soon ...

Source code

 

BQC++Toolbox

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BQC++Toolbox allows direct access to the Bisque DataBase system for C++ applications using Trolltech Qt library.

Requirements

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BioImage Convert

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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.

Features

  • Cross-platform with binaries for Windows, Mac, Linux
  • Reads many bio image and video formats
  • Exports several image and video formats
  • Reads and writes (OME-TIFF) meta-data
  • Applies many image operations: ROI, enhancement, depth convert, resize, rotate, channel remap, combine frames, etc...

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Source code

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bioView

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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.

Features

  • Cross-platform with binaries for Windows, Mac, Linux
  • Reads many bio image and video formats
  • Reads meta-data from BioRad PIC, TIFF, Metamorph STK (uncompressed and LZW compressed), Fluoview TIFF, Carl Zeiss LSM 5, PSIA TIFF, Nanoscope II/III
  • On-the-fly visualization (mapping/enhancement) of multi-channel data

Downloads

Please, refer to our paper if you use this software.

Documentation

Source code

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bioView3D

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bioView3D is an open source and cross-platform application intended for biologists to visualize 3D stack (laser scanning confocal, etc.) imagery. It runs on Windows, MacOS X and Linux.

Features

  • Cross-platform with binaries for Windows, Mac, Linux
  • Reads many bio image and video formats
  • Reads meta-data from BioRad PIC, TIFF, Metamorph STK (uncompressed and LZW compressed), Fluoview TIFF, Carl Zeiss LSM 5, PSIA TIFF, Nanoscope II/III
  • Has two modes of rendering: textures and voxels
  • On-the-fly 3D visualization (mapping/enhancement) of multi-channel data
  • Export of fly-over video to several popular formats: QuickTime, WMV, AVI, Flash, MPEG1/2/4, etc.
  • Visualization of graphical annotations: XML GObjects

Downloads

Please, refer to our paper if you use this software.

Documentation

Source code

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