ATF is a tab-delimited text file format that can be read by typical spreadsheet programs
such as Microsoft Excel. It is used for GenePix Array List (GAL) files,
and GenePix Results (GPR) files.
An ATF text file consists of records. Each line in the text file is a record.
Each record may consist of several fields, separated by a field separator
(column delimiter). The tab and comma characters are field separators. Space characters
around a tab or comma are ignored and considered part of the field separator. Text strings
are enclosed in quotation marks to ensure that any embedded spaces, commas and tabs
are not mistaken for field separators.
The group of records at the beginning of the file is called the file header. The
file header describes the file structure and includes column titles, units, and comments.
ATF File Structure
First header record Format: ATF (all caps), Version number
Second header record Number of optional header records n,
Number of data columns (fields) m
1st optional record ...
2nd optional record ...
nth optional record ...
(n+3)th record Required record containing m fields.
Each field contains a column title.
DATA RECORDS Arranged in m columns (fields) of data.
See below under GenePix Array List format for an example of an ATF file.
GenePix Array List files describe the size and position of blocks, the layout of
feature-indicators in them, and the names and identifiers of the printed substances
associated with each feature-indicator.
GenePix Pro includes an integrated Array List Generator which generates GAL files
from plain text files; see the GenePix Pro online Help for details.
GAL files conform to the Axon Text File (ATF) format described above.
As such, they can be created in Microsoft Excel by saving an Excel spreadsheet as Text
(Tab delimited).
To create a GAL file that describes block and feature-indicator positions and geometry,
but without substance IDs or names, save a settings file using the Save Settings As
command in GenePix Pro (select *.gal as the output file type).
GAL files consist of two sections: the header, and data records. The
header contains all the structural and positional information
about the blocks; the data records contain all the name and
identifier information for each spot.
GenePix Pro assigns block numbers such that the top leftmost block on the image is
block #1, and the block numbers increase from left to right and then from top to bottom:
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
The order in which a block was created does not matter;
GenePix Pro automatically renumbers all blocks to follow this rule.
Example GenePix Array List (GAL) file
The following very simple array list file describes four blocks ("BlockCount=4"),
each with 24 columns and 5 rows. For simplicity, we have included the data record
information (name, ID, etc) only for the first two features:
The header section describes basic file information and all block properties apart from
names and IDs (which are in the data records section). Each record
is explained below:
(Optional) The position and dimensions of each block. There is
one record for each block, and each record contains 7 fields. Each field is
separated by a comma followed by a space.
xOrigin
X position of center of top leftmost feature of current block (in µm).
yOrigin
Y position of center of top leftmost feature of current block (in µm).
FeatureDiameter
Diameter of features within the current block (in µm).
xFeatures
Number of columns of features in current block.
xSpacing
Column spacing of current block (in µm).
yFeatures
Number of rows of features in current block.
ySpacing
Row spacing of current block (in µm).
Note: Positions on arrays are measured in microns with
respect to the origin, which is the top left corner of the array.
(Optional) You may include any number of correctly formatted extra lines
in the header. When the GAL file is read as input by GenePix Pro 4.1, these will be
passed to the output Results (GPR) file.
(Required) Last line of the header, containing column titles
for the data records. The quotation marks are advised, but not necessary.
Description of data records
The Data Record section contains records which describe each feature in detail. It
includes the block, column, and row numbers for features, as well as descriptive name
and identifier information. The GAL Data Record may also optionally contain user-defined
fields (column titles) for extra annotation information that you may wish to include.
In GenePix Pro 4.1, any user-defined GAL file data columns are read and output to the
Results (GPR) file; in earlier versions they are ignored. Also new in GenePix Pro 4.1
is that there is no longer a 40-character limit on the Name and ID fields;
entries longer than 40 characters are truncated when read by earlier versions.
There is one record for each feature, containing a field for each of the descriptive columns:
Block
(Required) The block number for the feature (required).
Column
(Required) The column location within the block (required).
Row
(Required) The row location within the block (required).
Name
(Optional) Name to be displayed for the given feature (optional; limited to 40 characters in GenePix Pro 4.0 and earlier, no limit in 4.1).
ID
(Required) Identifier for each feature (required; limited to 40 characters in GenePix Pro 4.0 and earlier, no limit in 4.1).
"User Defined"
(Optional) Annotation information (optional).
Block, Column, Row and ID are required fields.
The column titles can be in any order.
Note: If you have empty features, use 'empty' as the feature ID,
and the feature is flagged absent when the GAL file is opened by GenePix.
A minimal GAL file header
Because most of the GAL file header records are optional, it is relatively
simple to construct a GAL file with a very minimal header. The following
example also leaves out the Name column, which is also optional:
When you open this GAL file in GenePix, you will be prompted with the New Blocks
dialog box to enter block properties. You may find this method of configuring
blocks via the New Blocks dialog box more convenient than working out block
arrangements by hand.
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.
GenePix acquisition, analysis and display settings are saved as binary GenePix
Settings Files. Settings are organized into a number of different categories
(acquisition, analysis and display) all of which are saved together in the GPS
file. However, when opening a settings file you can choose which subset of the
settings you wish to open.
Acquisition settings include which laser was enabled during the acquisition, the PMT
voltages, the lines averaged, and the scan area. Analysis settings include the
location and identification of blocks and feature-indicators that were defined on the
image. Display settings include brightness and contrast settings, and the color mapping.
Images can be saved in the JPEG format, which is a lossy compressed image file format.
GenePix implements minimal JPEG compression, which is enough to reduce image file size
significantly, but which removes only a small amount of data from the image. However,
we recommend that you do not use the JPEG format to archive images that are to be
analyzed later. Rather, use the JPEG format to store images that are to be used in
presentations.
Images acquired in GenePix are by default saved as 16-bit unsigned TIFF images.
This is a standard, uncompressed graphic file format that can be read by many graphics
and imaging programs. The primary data acquired by GenePix are the single-wavelength
images, and by default these are saved as 16-bit grayscale TIFFs in a single multi-image
TIFF file. Not all graphics applications can read multi-image TIFF files. You may wish
to try opening a multi-image file with your preferred graphics application to see if they
are supported. If not, save the single-wavelength images as separate single-image files.
GenePix exports its preview and pseudocolor ratio images as 24-bit color TIFFs, but it
does not read them, as data are not extracted from them.
GenePix Pro sets the following standard TIFF fields using the function call TIFFSetField():
Note: Any text in ALL CAPS is a constant defined in 3rd party file tiff.h (from Silicon Graphics).
TIFFTAG_IMAGEWIDTH
Image Width (pixels)
TIFFTAG_IMAGELENGTH
Image Height (pixels)
TIFFTAG_SUBFILETYPE
0
TIFFTAG_BITSPERSAMPLE
Bits Per Sample
TIFFTAG_SAMPLESPERPIXEL
Samples Per Pixel
TIFFTAG_ROWSPERSTRIP
Rows per strip (32)
TIFFTAG_PHOTOMETRIC
photometric interpretation
TIFFTAG_ORIENTATION
ORIENTATION_TOPLEFT (top left)
TIFFTAG_PLANARCONFIG
PLANARCONFIG_CONTIG (single image plane)
TIFFTAG_RESOLUTIONUNIT
RESUNIT_CENTIMETER (metric)
TIFFTAG_XRESOLUTION
X Resolution
TIFFTAG_YRESOLUTION
Y Resolution
TIFFTAG_XPOSITION
X Origin (resolution units)
TIFFTAG_YPOSITION
Y Origin (resolution units)
TIFFTAG_MINSAMPLEVALUE
Min Sample Value
TIFFTAG_MAXSAMPLEVALUE
Max Sample Value
TIFFTAG_SAMPLEFORMAT
SAMPLEFORMAT_UINT (1);
TIFFTAG_IMAGEDESCRIPTION
User comment
TIFFTAG_COMPRESSION
COMPRESSION_NONE or COMPRESSION_LZW or COMPRESSION_JPEG
TIFFTAG_JPEGQUALITY
Compression Factor (Only if TIFFTAG_COMPRESSION = COMPRESSION_JPEG)
TIFFTAG_AXON_IMAGEPARAMS
Text string giving GPP specific values, e.g., "AxImageIO: FullSize=550,1787; Compression=1,100; PMT=500; Averaging=1; LaserPower=3.51; LaserOnTime=39546; ScanPower=100; NormalizationFactor=1.000; Filter=<Empty>".
