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Tuesday, January 29th
12:00 – 1:00pm
105 Annenberg
*Lunch will be provided*
SPEAKER:
Alexandre Cunha
Center for Advanced Computing Research and Elliot Meyerowitz Lab, Caltech
TITLE:
Collaborative Image Analysis with the Masses: Challenges and Opportunities
ABSTRACT:
Extracting reliable quantitative information from digital images in an automatic fashion continues to be a difficult task. In many situations classical and contemporary algorithms only provide partial and sub-optimal results that might not be sufficient to carry on research studies thus leading practitioners to rely on manual annotations. We present our work on collaborative image segmentation, an online crowdsourcing system where computers, experts, and non-experts cooperate to produce robust results supporting the research of plant biologists. We address some of the technical and nontechnical challenges in building such a system and discuss the potential in employing the vision of crowds to help solve image processing problems which are still poorly solved by computers alone.
This is a work in progress in collaboration with Elliot Meyerowitz lab at Caltech and with Tsang Ing Ren lab at UFPE, Brazil.
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Co-Sponsored by the Caltech Biological Network Modeling Center (BNMC)
Gustavo Kunde Rohde, Assistant Professor, Biomedical Engineering, Carnegie Mellon University
Monday, May 16, 2011
2:00 PM – 3:00 PM
Beckman Institute Auditorium
Novel biomedical imaging techniques have enabled the acquisition of quantitative information from cells, tissues, and organs with unprecedented accuracy and specificity. Combined with the availability of vast computational resources, quantitative biomedical imaging pipelines have the potential to accelerate scientific discovery and improve clinical practice. An important engineering problem in this area relates to extracting quantitative information related to the form (shape and texture) of cells, tissues, and organs. I will describe our recent efforts toward the development of a general purpose segmentation method and present preliminary evidence that a tool capable of high-enough accuracy for quantitative imaging pipelines may one day be available. In addition, recent efforts in developing geometric data analysis tools for mining morphological information from biomedical image data will be described. In particular, I will describe the application of deformation and transportation related metrics, in combination with discriminant analysis techniques, towards understanding the distribution of cellular patterns in cancerous and normal tissues.
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CACR Publication News: Cellcenter collaboration with developmental biologists yields insight in fruit fly genomics
“High resolution mapping of Twist to DNA in Drosophila embryos: Efficient functional analysis and evolutionary conservation” was published in the Genome Research Journal, Advanced Online Access, March 2011. Genome Research focuses on research that provides novel insights into the genome biology of all organisms, including advances in genomic medicine.
From the abstract:
“Cis-regulatory modules (CRMs) function by binding sequence specific transcription factors, but the relationship between in vivo physical binding and the regulatory capacity of factor-bound DNA elements remains uncertain. We investigate this relationship for the well-studied Twist factor in Drosophila melanogaster embryos by analyzing genome-wide factor occupancy and testing the functional significance of Twist occupied regions and motifs within regions … Our results show that high resolution in vivo occupancy data can be used to drive efficient discovery and dissection of global and local cis-regulatory logic.” (more)
CACR staff member Shirley Pepke analyzed the ChIP-seq binding data and found enhanced evolutionary conservation associated with candidate cis regulatory modules.
About Cellcenter: The goal of the Center for Integrative Study of Cell Regulation (Cell Center) is to develop new computational methods for understanding how the many genes and proteins that make up individual cells work together to carry out specialized functions of different cell types, including neurons, plant cells, and bacteria. See www.cellcenter.caltech.edu for further information.
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Researchers in Caltech’s Biological Networking Modeling Center (BNMC) and their collaborators have released the first standard graphical notation for biology. The new standard, called the Systems Biology Graphical Notation (SBGN), was published in the August 8 issue of the journal Nature Biotechnology. BNMC was founded to encourage closer interactions between the Division of Biology, Control & Dynamical Systems, and CACR.
Read more in the Caltech Press Release
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Monday, Oct. 27, 11:00AM
Moore 080
“Models of interactions of Ca(2+), CaM, and monomeric catalytic subunits of CaMKII: a piece of the post-synaptic signaling network puzzle”
Dr. Shirley Pepke, Caltech Center for Advanced Computing Research Read more »
