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UCSF Spot | Fully automatic quantification of microarray image data


A package for a quantitative assessment of performance on multiple replicates of genome-wide array-based comparative genomic hybridization experiments. UCSF Spot automatically locates both subarray grids and individual spots. Ratios are computed based on explicit segmentation of each spot. On a typical image of 6000 spots, the entire process takes less than 20 sec. UCSF Spot offers a step toward fast and accurate operator-independent results in the quantification of DNA microarray image data.

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UCSF Spot classification

UCSF Spot specifications

Unique identifier:
Graphical user interface
Input data:
Geometry of subarray grids and the geometry of spots in each subarray
Programming languages:
Software type:
Restrictions to use:
Academic or non-commercial use
Operating system:
Unix/Linux, Windows
Computer skills:

UCSF Spot distribution


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Comprehensive Cancer Center, University of California, San Francisco, CA, USA; Cancer Research Institute, University of California, San Francisco, CA, USA; Department of Laboratory Medicine, University of California, San Francisco, CA, USA

Funding source(s)

This work was supported in part by grants from the National Cancer Institute (CA83040, CA89520, and CA64602).

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