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Research News
Cover of May Issue of PLoS Biology
2D confocal projection image of Arabidopsis thaliana adaxial sepal epidermal nuclei.
Software News
Moving to Google Code!!!
I'm moving all my projects to Google Code for the Mercurial source repositories :)
Software
Cite this site: Boguslaw Obara, BioImage Informatics, http://boguslawobara.net
| Segmentation | Bio-DataBase | Filtering | Shape Matching | Shape Analysis | Computational Geometry | Utilities |
Segmentation
BOTracingCurvilinearStructures
Algorithm for tracing curvilinear structures, based on local variations of intensity along the traced curve.
BOParamCurvilinearStructure
Algorithm for determining a set of parameters characterizing the curvilinear structure.
BONucleiDetector3D
This application allows you to automatically identify nuclei centroid locations in 3D.
BONucleiDetector2D
This application allows you to automatically identify nuclei centroid locations in 2D.
BOCurvatureEstimation ByOsculatingCircle
Algorithm for curvature estimation of digital curves based on osculating circle.
BOMicrocracksSandstone
Standard segmentation of microcracks observed on microscope images of sandstone thin sections.
Bio-DataBase
I am one of the core developers of the BISQUE system (Bio-Image Semantic Query User Environment). BISQUE is an ongoing project with the goal of providing an online platform for data exchange and exploration of biological images. Some of the tools we have developed:
BQBisqueJ
BQBisqueJ is an ImageJ plugin that allows you to access the BISQUE.
BQBisqueJ_.java - ImageJ plugin.
BQJavaLib - Java library (jv 1.6).
BQJavaLib
BQJavaLib is an Java library for Matlab that allows you to access the BISQUE.
BQMatlabStart.m - Matlab demo.
BQJavaLib - Java library for Matlab.
BQMatlabToolbox
BQMatlabToolbox is a Matlab toolbox that allows you direct access to the BISQUE system.
BQMatlabToolbox.m - Matlab file.
BQJavaLib - Java library for Matlab.
BQMatlabToolbox requirements:
- Matlab Image Processing Toolbox,
- javac - included in JDK from Sun Microsystems, open-sourced, Sun Java SE.
Filtering
Shape Analysis
Shape Matching
BOLogPolarHist
Matlab/C++ MEX code for Log-Polar Histogram, according to:
S. Belongie, J. Malik and J. Puzicha: Shape Matching and Object Recognition using Shape Context
IEEE Trans. on Pattern Analysis and Machine Intelligence, Vol. 24, No. 24, pp. 509-522, 2002.
BOLap
Matlab/C++ MEX code for Linear Assignment Problem, according to:
R. Jonker and A. Volgenant: A Shortest Augmenting Path Algorithm for Dense and Sparse Linear Assignment Problems
Computing 38, 325-340, 1987
BOCostFunction
Matlab/C++ MEX code for calculating of cost function from 2 Log-Polar Histograms.
Utilities
Computational Geometry
BOPointInPolygon
Matlab function for calculating of query point position in polygon.