The BioImaging Group

Life Sciences Division

Lawrence Berkeley National Laboratory

One Cyclotron Road, MS 84-171, Berkeley, CA 94720


The BioImaging Group develops statistical, image analysis and visualization methods for unraveling basic mechanisms of biology. We are particularly interested in multicellular systems and assembling quantitative system-wide information derived at cellular and subcellular resolution. 


The Berkeley Drosophila Transcription Network Project
The NuMA Project: Early Detection of Mammary Cancer

The Lab, Family & Friends

The Alfa Lab

The view is clear from up here

Recent Publications

  1. Stewart MacArthur, Xiao-Yong Li, Jingyi Li, James B. Brown, Hou Cheng Chu, Lucy Zeng, Brandi P. Grondona, Aaron Hechmer, Lisa Simirenko, Soile V.E. Keränen, David W. Knowles, Mark Stapleton, Peter Bickel, Mark D. Biggin and Michael B. Eisen 2009
    Functionally distinct transcription factors show a quantitative continuum of binding and function to highly overlapping sets of thousands of genomic regions in the Drosophila melanogaster blastoderm Genome Biology 2009 In Press
  2. G.H. Weber, O. Rübel, M.-Y. Huang, A.H. DePace, C.C. Fowlkes,S.V.E. Keränen, C.L. Luengo Hendriks, H. Hagen, D.W. Knowles, J. Malik,M.D. Biggin, B. Hamann, 2009
    Visual exploration of three-dimensional gene expression using physical views and linked abstract views
    Computational Biology and Bioinformatics,IEEE/ACM, Transactions on. 6:296-309, 2009 [Reprint]
  3. Charless C. Fowlkes, Cris L. Luengo Hendriks, Soile V.E. Keränen, Gunther H. Weber, Oliver Rübel, Min-Yu Huang, Sohail Chatoor, Angela H. DePace, Lisa Simirenko, Clara Henriquez, Amy Beaton, Richard Weiszmann, Susan Celniker, Bernd Hamann, David W. Knowles, Mark D. Biggin, Michael B. Eisen, J. Malik, 2007
    A quantitative spatio-temporal atlas of gene expression in the Drosophila blastoderm
    Cell 133(2):364-374
  4. X. Li, S. MacArthur, R. Bourgon, D. Nix, D.A. Pollard, V.N. Iyer, A. Hechmer, L. Simirenko, M. Stapleton, C.L. Luengo Hendriks, H.C. Chu, N. Ogawa, W. Inwood, V. Sementchenko, A. Beaton, R. Weiszmann, S.E. Celniker, D.W. Knowles, T. Gingeras, T.P. Speed, M.B. Eisen and M.D. Biggin, Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm
    PLoS Biology 6(2):e27
  5. Cris L. Luengo Hendriks, Soile V.E. Keränen, Mark D. Biggin, David W. Knowles, 2007
    Automatic channel unmixing for high-throughput quantitative analysis of fluorescence images
    Optics Express 15(19):12306-12317
  6. Fuhui Long, Hanchuan Peng, Damir Sudar, Sophie A. Lelièvre, David W. Knowles, 2007
    Phenotype Clustering of Breast Epithelial Cells in Confocal Images based on Nuclear Protein Distribution Analysis
    BMC Cell Biology 8(Suppl 1):S3
  7. Gurushankar Chandramouly, Patricia C. Abad, David W. Knowles, Sophie A. Lelièvre, 2007
    The control of tissue architecture over nuclear organization is crucial for epithelial cell fate
    Journal of Cell Science 120:1596-1606
  8. Patricia C. Abad, Jason Lewis, I. Saira Mian, David Knowles, Jennifer Sturgis, Sunil Badve, Jun Xie, Sophie A. Lelièvre, 2007
    NuMA Influences Higher Order Chromatin Organization in Human Mammary Epithelium
    Mol. Biol. Cell 18:348-361
  9. Cris L. Luengo Hendriks, David W. Knowles, 2007.
    Comments on a novel 3D wavelet-based filter for visualizing features in noisy biological data
    Journal of Microscopy 225:104-107
  10. Cris L. Luengo Hendriks, Soile V.E. Keränen, Charless C. Fowlkes, Lisa Simirenko, Gunther H. Weber, Clara Henriquez, David W. Kaszuba, Bernd Hamann, Michael B. Eisen, Jitendra Malik, Damir Sudar, Mark D. Biggin, and David W. Knowles, 2006
    3D Morphology and Gene Expression in the Drosophila Blastoderm at Cellular Resolution I: data acquisition pipeline
    Genome Biology 7:R123.
  11. Soile V.E. Keränen, Charless C. Fowlkes, Cris L. Luengo Hendriks, Damir Sudar, David W. Knowles, Jitendra Malik, and Mark D. Biggin, 2006
    3D Morphology and Gene Expression in the Drosophila Blastoderm at Cellular Resolution I: dynamics
    Genome Biology 7:R124.
  12. David W. Knowles, Damir Sudar, Carol Bator-Kelly, Mina J. Bissell, and Sophie A. Lelièvre, 2006.
    Automated local bright feature image analysis of nuclear protein distribution identifies changes in tissue phenotype
    Proc. Natl. Acad. Sci. USA 103:4445-4450
  13. O. Rübel, G.H. Weber, S.V.E. Keränen, C.C. Fowlkes, C.L. Luengo Hendriks, L. Simirenko, N.Y. Shah, M.B. Eisen, M.D. Biggin, H. Hagen, D. Sudar, J. Malik, D.W. Knowles and B. Hamann, 2006
    PointCloudXplore: Visual Analysis of 3D Gene Expression Data Using Physical Views and Parallel Coordinates
    in: H. Hagen, A. Kerren and P. Dannenmann (eds.), Visualization of Large and Unstructured Data Sets, Lecture Notes in Informatics, Vol. S-4, pp. 107-117, Gesellschaft für Informatik, Bonn.


The BioImaging Group is:

David W. Knowles
David W. Kaszuba
Soile Keränen
Bjorn Ommer
Gunther H. Weber
Oliver Rübel
Min-Yu Huang


Mark Biggin, Genomics Division, LBNL
Jitendra Malik, EECS, University of California at Berkeley
Charless Fowlkes, CS, University of California at Irvine
Bernd Hamann, Institute for Data Analysis and Visualization, University of California at Davis
Michael Eisen, Lisa Simirenko, Genomics Division, LBNL
Angela DePace, Department of Systems Biology, Harvard Medical School
Mina Bissell, Life Sciences Division, LBNL
Sophie Lelièvre, Basic Medical Sciences Deptartment, Purdue University
Sunil Badve, Indiana University School of Medicine
Jian Jin, Center for Systems Biology Engineering, LBNL
James Sethian, Dept. of Mathematics, Univ. of California, Berkeley, and Head, Mathematics Department, Lawrence Berkeley National Laboratory


Cris L. Luengo Hendriks,  Center for Image Analysis, Uppsala, Sweden
Angela DePace, Systems Biology, Harvard Medical School
Charless Fowkles, Computer Vison, UC Irvine
Fuhui Long, Janelia Farm, Howard Hughes Medical Institute, Virginia
Hanchuan Peng, Janelia Farm, Howard Hughes Medical Institute, Virginia
Jennifer Gong
Sohail Chatoor
Damir Sudar, LBNL
Carlos Ortiz de Solórzano, CIMA, University of Pamplona, Spain

Our BDTNP collaborators (2005)