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ITCN

Semi-automatic image segmentation & annotation NEW!!!

Overview: This is a set of MATLAB scripts for semi-automatic image segmentation & annotation. It uses a segmentation algorithm to preprocess the image and allows the user to recombine, refine and create segments and to label them out of a set of given categories.

Requirements: This tool was successfully tested under Linux and MS Windows. It requires ImageMagick to convert image formats, please install it from http://www.imagemagick.org and make sure your system can call the 'convert' command.

Description: As a preprocessing step, this tool uses the segmentation algorithm described in: Efficient Graph-Based Image Segmentation Pedro F. Felzenszwalb and Daniel P. Huttenlocher International Journal of Computer Vision, 59(2) September 2004. A compiled version for Linux and MS Windows is included, however, the source code can be obtained online: http://people.cs.uchicago.edu/~pff/segment/

» SegmentationforCortina.zip

ITCN

Threaded and Templated C++ K-Means Clustering Library

Features: a) easy to use C++ Templated code, b) cross-platform, c) threaded execution, performs faster on multi-core systems d) Several distance functions implemented: euclidean, squared euclidean, manhattan, chebychev, EMD, e) Easy extension for different initialization functions, with implemented Even and random with minimum distance between centroids.

Specialized classes for HTD feature vectors I/O and clustering.

» clusterTextures.zip

Bio-imaging software

Scientist's Digital Notebook UPDATED!!!

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: a) User-defined meta-data annotations, b) Powerful graphical annotations with user-defined types, c) Bio-formats meta-data and file name parsing, d) Rapid upload for Bisque database, e) In-place simple statistics for graphical annotations

Downloads

Documentation

Source code

 

bioView3D NEW!!!

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

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Documentation

Source code

bioView UPDATED!!!

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

Downloads

Documentation

Source code

 

BioImage Convert UPDATED!!!

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, Metamorph STK (uncompressed and LZW compressed), Fluoview TIFF, 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: a) Cross-platform with binaries for Windows, Mac, Linux, b) Reads many bio image and video formats, c) Exports several image and video format, d) Reads meta-data, e) Applies many image operations: ROI, enhancement, depth convert, resize, rotate, channel remap, combine frames, etc...

Downloads

Matlab 7 interface for bioimage convert library

Documentation

Source code

 

ITCN

ITCN: Automatic Nuclei Counter plug-in for ImageJ

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

Required Downloads

Documentation

Datasets

This web site organizes the datasets collected by Vision Research Lab. As more and more datasets are collected from the internet and other resources, we are facing a challenge of managing the data for our research and other uses. We hope that researchers will have complete knowledge of what the data resources we have and how to access the data.

Aerial photos

A collection of 40 large aerial photos is mainly used to investigate the image texture features.

Aerial photos (128x128 tiles)

In this dataset, one large aerial photo is divided into 128x128 tiles. The total number of tiles is 54,013. Two image formats are available, .raw and .jpg. Texture feature vector is extracted for each tile.

» Images: [RAW, JPG]

» Texture Feature Vectors: [48, 50, 60] dimensions

Aerial photos (64x64 tiles)

Each large aerial photo is divided into 64x64 tiles. The total number of tiles is 275,465. Images are available in two formats, .raw and .jpg.

» Images: [RAW, JPG]

» Feature vectors: [Texture feature vectors, Normalized texture features]

» 60 dimensional raw and normalized feature vectors: [Aerial40.txt, Aerial_norm40.txt, Extract_feature.c]