Bioimage Analysis Toolbelt

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Welcome! This site contains a tutorial, citations, and Matlab code for a set of bioimage analysis applications.

Module 0: Download Lecture

• Introduction

Module 1: Download Lecture

• Active contours for segmentation [code] [paper]
  
• Bing Li; Acton, S.T.; , "Active Contour External Force Using Vector Field Convolution for Image Segmentation," Image Processing, IEEE Transactions on , vol.16, no.8, pp.2096-2106, Aug. 2007
  doi: 10.1109/TIP.2007.899601
• Active contours for tracking [code] [paper]
• Ray, N.; Acton, S.T.; Ley, K.; , "Tracking leukocytes in vivo with shape and size constrained active contours," Medical Imaging, IEEE Transactions on , vol.21, no.10, pp.1222-1235, Oct. 2002
  doi: 10.1109/TMI.2002.806291

Module 2: Download Lecture

• Scale space for segmentation [code Anisotropic Diffusion] [code SRAD] [paper]
• Yongjian Yu; Acton, S.T.; , "Speckle reducing anisotropic diffusion," Image Processing, IEEE Transactions on , vol.11, no.11, pp.1260- 1270, Nov 2002
  doi: 10.1109/TIP.2002.804276

Module 3: Download Lecture

• Graph theoretic segmentation of filamentous objects [code] [paper]
• Basu, Saurav; Aksel, Alla; Condron, Barry; Acton, Scott T.; , "Tree2Tree: Neuron segmentation for generation of neuronal morphology," Biomedical Imaging: From Nano to Macro, 2010 IEEE International Symposium on , vol., no., pp.548-551, 14-17 April 2010
  doi: 10.1109/ISBI.2010.5490289
• Graph cuts for segmentation [paper]
• to appear in Image Analysis & Interpretation (SSIAI), 2012 IEEE Southwest Symposium on

Module 4: Download Lecture

• Particle filters for tracking [code] [paper]
• Cui, Jing; Acton, S.T.;, Lin, Z.; , "A Monte Carlo approach to rolling leukocyte tracking in vivo.," Medical Image Analisys , vol.10, no.4, pp.598-610, Aug. 2006
  doi: 10.1016/j.media.2006.05.006

Module Bonus: Download Lecture

• Kalman filter for tracking [code] [paper]
• Acton, Scott T.; Wethmar, Klaus; Ley, K.; , "Automatic tracking of rolling leukocytes in vivo.," Microvascular research , vol.63, no.1, pp.139-148, Jan. 2002
  doi: 10.1006/mvre.2001.2373

Instructions

Each zipped file is a directory with code and a sample data set:

1. Unzip the directory
2. Upen MATLAB and change to that directory
3. If a file named compile.m exists, type:
   compile (at the MATLAB prompt)
(This file fill automatically compile any C/C++ code. Installation of compilers may be necessary for your machine. You may have to run "mex -setup" if you have never used mex before. You may need help getting this started if you are not the programming geek type!)
4. To run the example code type:
   example (if you are using a PC)
   examplemac (if you are using a MAC)
   

All the code on this website is distributed under the GNU General Public License, which specifies the conditions under which it may be modified and redistributed. This license ensures the freedom of the software and allows for the distribution of modified copies in a manner that is consistent with that freedom. Please read it carefully. If you have further questions, please refer to the software license pages at the Free Software Foundation website. These files are not guaranteed to work on your machine and are not supported.