GenePix® Pro 文件格式

GenePix® Pro 文件格式

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GPR  -  GenePix Results format (*.gpr)

GenePix Results data are saved as GPR files, which are in  Axon Text File (ATF) format. A Results file contains general information about image acquisition and analysis, as well as the data extracted from each individual feature. Any user-defined feature data contained in a GAL file read by GenePix Pro 4.1 will be included in the output GPR file. As of GenePix Pro version 4.0.1.4, the GPR version number is 3.0.

Read a history of the changes to the GPR file format since GenePix Pro 3, including example GPR files in all the various formats.

GPR Header

A sample GPR file header and a description of each entry are shown below:

Entry	Description
ATF     1.0	File type and version number.
29       48	Number of optional header records and number of data fields (columns).
"Type=GenePix Results 3"	Type of ATF file.
"DateTime=2002/02/09 17:15:48"	Date and time when the image was acquired.
"Settings=C:\Genepix\Genepix.gps"	The name of the settings file that was used for analysis.
"GalFile=C:\Genepix\Demo.gal"	The GenePix Array List file used to associate Names and IDs to each entry.
"PixelSize=10"	Resolution of each pixel in µm.
"Wavelengths=635     532"	Installed laser excitation sources in nm.
"ImageFiles=C:\Genepix\demo.tif 0 C:\Genepix\Genepix.tif 1"	The name and path of the associated TIF file(s).
"NormalizationMethod=None"	The type of normalization method used, if applicable.
"NormalizationFactors=1    1"	The normalization factor applied to each channel.
"JpegImage=C:\Genepix\demo.jpg"	The name and path of the associated Jpeg image files.
"StdDev=Type 1"	The type of standard deviation calculation selected in the Options settings.
"RatioFormulation=W1/W2 (635/532)"	The ratio formulation of the ratio image, showing which image is numerator and which is denominator.
"Barcode=00331"	The barcode symbols read from the image.
"BackgroundSubtraction=LocalFeature"	The background subtraction method selected in the Options settings.
"ImageOrigin=0, 0"	The origin of the image relative to the scan area.
"JpegOrigin=390, 4320"	The origin of the Results JPEG image (the bounding box of the analysis Blocks) relative to the scan area origin.
"Creator=GenePix 4.1.1.4"	The version of the GenePix Pro software used to create the Results file.
"Scanner=GenePix 4000B [serial number]"	Type and serial number of scanner used to acquire the image.
"FocusPosition=0"	The focus position setting used to acquire the image, in microns.
"Temperature=19.6127"	The temperature of the scanner, in degrees C.
"LinesAveraged=1"	The line average setting used to acquire the image.
"Comment=hyb 2673"	User-entered file comment.
"PMTGain=500     600"	The PMT settings during acquisition.
"ScanPower=100    100"	The amount of laser transmission during acquisition.
"LaserPower=1    1"	The power of each laser, in volts.
"LaserOnTime=5    5"	The laser on-time for each laser, in minutes.
"Filters=<Empty>    <Empty>"	Emission filters used during acquisition (GenePix 4100 and 4200 only.)
"ScanRegion=100,100,2000,2000"	The coordinate values of the scan region used during acquisition, in pixels.
"Supplier="	Header field supplied in GAL file.
Data record column headings	Column titles for each measurement (see below).
Data Records	Extracted data.

 

GPR Data

The list below describes each column of data in the Results file.

Column Title	Description
Block	the block number of the feature.
Column	the column number of the feature.
Row	the row number of the feature.
Name	the name of the feature derived from the Array List (up to 40 characters long, contained in quotation marks).
ID	the unique identifier of the feature derived from the Array List (up to 40 characters long, contained in quotation marks).
X	the X-coordinate in µm of the center of the feature-indicator associated with the feature, where (0,0) is the top left of the image.
Y	the Y-coordinate in µm of the center of the feature-indicator associated with the feature, where (0,0) is the top left of the image.
Dia.	the diameter in µm of the feature-indicator.
F635 Median	median feature pixel intensity at wavelength #1 (635 nm).
F635 Mean	mean feature pixel intensity at wavelength #1 (635 nm).
F635 SD	the standard deviation of the feature pixel intensity at wavelength #1 (635 nm).
B635 Median	the median feature background intensity at wavelength #1 (635 nm).
B635 Mean	the mean feature background intensity at wavelength #1 (635 nm).
B635 SD	the standard deviation of the feature background intensity at wavelength #1 (635 nm).
% > B635 + 1 SD	the percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength #1 (635 nm).
% > B635 + 2 SD	the percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength #1 (635 nm).
F635 % Sat.	the percentage of feature pixels at wavelength #1 that are saturated.
F532 Median	median feature pixel intensity at wavelength #2 (532 nm).
F532 Mean	mean feature pixel intensity at wavelength #2 (532 nm).
F532 SD	the standard deviation of the feature intensity at wavelength #2 (532 nm).
B532 Median	the median feature background intensity at wavelength #2 (532 nm).
B532 Mean	the mean feature background intensity at wavelength #2 (532 nm).
B532 SD	the standard deviation of the feature background intensity at wavelength #2 (532 nm).
% > B532 + 1 SD	the percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength #2 (532 nm).
% > B532 + 2 SD	the percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength #2 (532 nm).
F532 % Sat.	the percentage of feature pixels at wavelength #2 that are saturated.
Ratio of Medians	the ratio of the median intensities of each feature for each wavelength, with the median background subtracted.
Ratio of Means	the ratio of the arithmetic mean intensities of each feature for each wavelength, with the median background subtracted.
Median of Ratios	the median of pixel-by-pixel ratios of pixel intensities, with the median background subtracted.
Mean of Ratios	the geometric mean of the pixel-by-pixel ratios of pixel intensities, with the median background subtracted.
Ratios SD	the geometric standard deviation of the pixel intensity ratios.
Rgn Ratio	the regression ratio of every pixel in a 2-feature-diameter circle around the center of the feature.
Rgn R²	the coefficient of determination for the current regression value.
F Pixels	the total number of feature pixels.
B Pixels	the total number of background pixels.
Sum of Medians	the sum of the median intensities for each wavelength, with the median background subtracted.
Sum of Means	the sum of the arithmetic mean intensities for each wavelength, with the median background subtracted.
Log Ratio	log (base 2) transform of the ratio of the medians.
Flags	the type of flag associated with a feature.
Normalize	the normalization status of the feature (included/not included).
F1 Median - B1	the median feature pixel intensity at wavelength #1 with the median background subtracted.
F2 Median - B2	the median feature pixel intensity at wavelength #2 with the median background subtracted.
F1 Mean - B1	the mean feature pixel intensity at wavelength #1 with the median background subtracted.
F2 Mean - B2	the mean feature pixel intensity at wavelength #2 with the median background subtracted.
SNR 1	the signal-to-noise ratio at wavelength #1, defined by (Mean Foreground 1- Mean Background 1) / (Standard deviation of Background 1)
F1 Total Intensity	the sum of feature pixel intensities at wavelength #1
Index	the number of the feature as it occurs on the array.
"User Defined"	user-defined feature data read from the GAL file (GenePix Pro 4.1).