Analysis of Biological and Medical Images

We seek to develop computational vision approaches to better understand various biological and medical problems. Our collaborators include the Lawrence Berkeley National Laboratory (LBNL) and the Fletcher Lab at UC Berkeley's Bioengineering Department. Two ongoing efforts with LBNL are the Berkeley Drosophila Transcription Network Project, building a morphological and gene expression atlas in Drosophila, and the ENIGMA Project, detecting and reconstructing molecular structures in Electron Microscopy images. We are also working with the Fletcher Lab to develop algorithms for low-cost automated disease diagnosis using images from the novel CellScope device.

Resources

  • TextonSVM: Automatic Particle Selection for Single Particle Analysis.

  • PCT: Automated Particle Correspondence and Accurate Tilt-axis Detection in Tilted-image Pairs.

Publications:

* "Automated Particle Correspondence and Accurate Tilt-axis Detection in Tilted-image Pairs".
M. Shatsky*, P. Arbelaez*, B.G. Han, D. Typke, S. Brenner, J. Malik. and R.M. Glaeser. (*equal contribution)
Journal of Structural Biology, 2014.
   [ pdf] [ online paper ] [project page]
* "Volumetric Semantic Segmentation using Pyramid Context Features"
J. Barron, P. Arbelaez, S. Keranen, M. Biggin, D. Knowles and J. Malik.
ICCV, 2013.   [pdf] [bibtex] [movie]
* "Automated Tuberculosis Diagnosis Using Fluorescence Images from a Mobile Microscope"
J. Chang, P. Arbelaez, N. Switz, C. Reber, A. Tapley, L. Davis, A. Cattamanchi, D. Fletcher, and J. Malik.
MICCAI, 2012.   [pdf] [code] [dataset] ;
* "Experimental Evaluation of Support Vector Machine-based and Correlation-based Approaches to Automatic Particle Selection".
P. Arbelaez, B.G. Han, D. Typke, J. Lim, R.M. Glaeser, and J. Malik.
Journal of Structural Biology, 2011.
doi:10.1016/j.jsb.2011.05.017    [pdf] [project page]
* "Constructing a quantitative spatio-temporal atlas of gene expression in the Drosophila blastoderm".
C. Fowlkes, C. Luengo Hendriks, S. Keränen, G. Weber, O. Rübel, M-Y Huang, S. Chatoor, L. Simirenko, A. DePace C. Henriquez, A. Beaton, R. Weiszmann, S. Celniker, B. Hamann, D. Knowles, M. Biggin, M. Eisen, and J. Malik.
Cell, 2008.    [pdf]
* "Expressing Genes"
Felice Frankel interviews A. DePace, G. Weber and C. Fowlkes.
American Scientist, 2007.   [pdf] 
* "3D Morphology and Gene Expression in the Drosophila Blastoderm at Cellular Resolution II: Dynamics".
S. Keränen, C. Fowlkes, C. Luengo Hendriks, D. Sudar, D. Knowles, J. Malik and M. Biggin.
Genome Biology, 2006.    [pdf]
* "3D Morphology and Gene Expression in the Drosophila Blastoderm at Cellular Resolution I: Data Acquisition Pipeline".
C. Luengo-Hendriks, S. Keränen, C. Fowlkes, L. Simirenko, G. Weber, C. Henriquez, D. Kaszuba, B. Hamann, M. Eisen, J. Malik, D. Sudar, M. Biggin and D. Knowles.
Genome Biology, 2006.    [pdf]
* "Inferring nuclear movements from fixed material"
C. Fowlkes and J. Malik.
Technical Report, U.C. Berkeley, 2006    [pdf]
* "Registering Drosophila Embryos at Cellular Resolution to Build a Quantitative 3D Map of Gene Expression Patterns and Morphology".
C. Fowlkes, C. Luengo Hendriks, S. Keränen, M. Biggin, D. Knowles, D. Sudar and J. Malik.
CSB 2005 Workshop on BioImage Data Minning and Informatics, 2005.    [pdf]


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Questions —> Pablo Arbelaez