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UCSF Spot specifications


Unique identifier OMICS_00849
Name UCSF Spot
Software type Package/Module
Interface Graphical user interface
Restrictions to use Academic or non-commercial use
Input data Geometry of subarray grids and the geometry of spots in each subarray
Operating system Unix/Linux, Windows
Programming languages C
Computer skills Medium
Stability Stable
Maintained Yes




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Publication for UCSF Spot

UCSF Spot citations


Genome wide copy number analysis of cerebrospinal fluid tumor cells and their corresponding archival primary tumors

Genom Data
PMCID: 4535622
PMID: 26484071
DOI: 10.1016/j.gdata.2014.04.003

[…] in the female test sample. post-hybridization imaging data and analysis of the bac array were done as previously described . the intensity values were used to calculate cy3/cy5 ratios using the ucsf spot program. an in-house r package ‘spot correction’ was also used to remove systematic variations of unknown origin across the array , including a correction that is based on the gc content […]


Integration of DNA Copy Number Alterations and Transcriptional Expression Analysis in Human Gastric Cancer

PLoS One
PMCID: 3335165
PMID: 22539939
DOI: 10.1371/journal.pone.0029824

[…] slides were mounted in mounting solutions containing 0.3 µg/ml dapi. three single-color intensity images (dapi, cy3 and cy5) were collected for each array using a charge coupled device camera., the ucsf spot software was used to automatically segment the spots based on the dapi images, perform local background corrections, and calculate various measurement parameters including log2 ratios […]


Isolation and genomic analysis of circulating tumor cells from castration resistant metastatic prostate cancer

BMC Cancer
PMCID: 3395839
PMID: 22373240
DOI: 10.1186/1471-2407-12-78

[…] 5-dctp (amersham), respectively. labeled test and reference dna were co-hybridized to a bac array. the arrays were imaged using a custom built ccd array imaging system [] and analyzed using the ucsf spot program to calculate cy3/cy5 ratios. the ucsf spot program is a fully automated system for microarray imaging that locates both subarray grids and individual spots []. ratios […]


An Adaptable, Portable Microarray Reader for Biodetection

PMCID: 3348790
PMID: 22574030
DOI: 10.3390/s90402524

[…] in detail in the experimental section., additional upgrades are possible to improve portability. first, a program automating all of the steps described above is needed, such as provided by the ucsf spot program []. with arrays in a fixed position relative to the detector, the same pixel numbers can be used every time to gather means and sds, or object-recognition software can be used […]


Genome position and gene amplification

Genome Biol
PMCID: 2394771
PMID: 17584934
DOI: 10.1186/gb-2007-8-6-r120

[…] colonies (cy3 labeled cdna). hybridizations were carried out on arrays of printed long oligonucleotides (70 mers) containing 21,000 elements (operon v2.0 []). array images were analyzed using ucsf spot software []. expression data were filtered to exclude all spots with foreground intensity below 500 units in the cy3 or cy5 channel and were subsequently median normalized and log2 […]


A large field CCD system for quantitative imaging of microarrays

Nucleic Acids Res
PMCID: 1456328
PMID: 16670425
DOI: 10.1093/nar/gkl160

[…] includes acquisition of a dapi image in addition to images of each of the fluorochromes used label the nucleic acids in the hybridization., array images were analyzed using the software package ucsf spot (). spot segments array elements based on either the dapi image or the hybridization images, determines the intensities of the hybridization signals, corrects the intensities for local […]

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UCSF Spot institution(s)
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
UCSF Spot funding source(s)
This work was supported in part by grants from the National Cancer Institute (CA83040, CA89520, and CA64602).

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