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Name

mar345_formats - description of image formats for images collected on a mar345 Imaging Plate Detector System.

Description

The 345 mm mar scanners produce the following image file formats:
compressed images ("MAR345"):
Transformed and corrected compressed images. The compression algorithm was kindly provided by Dr. J.P. Abrahams of the LMB in Cambridge, UK.
uncompressed images in old image format ("IMAGE"):
Transformed and corrected uncompressed images that are compatible with the formats of the 180 and 300 mm scanners (see mar_images).
spiral images ("SPIRAL"):
Raw data in spiral coordinates. Before using them in any crystallographic program they have to be transformed into a cartesian coordinate system. During transformation, corrections are applied.

Image Sizes

The mar345 scanner is able to scan the plate using 2 pixel sizes (0.10 mm or 0.15 mm), each at 4 different radii can be chosen, so that in total 8 different image sizes can be produced:

PixelsizeDiameterSIZEFile name extension
[mm] [mm]
0.15345.02300 * 2300.mar2300 or .pck2300
300.02000 * 2000.mar2000 or .pck2000
240.01600 * 1600.mar1600 or .pck1600
180.01200 * 1200.mar1200 or .pck1200
0.10345.03450 * 3450.mar3450 or .pck3450
300.03000 * 3000.mar3000 or .pck3000
240.02400 * 2400.mar2400 or .pck2400
180.01800 * 1800.mar1800 or .pck1800

Mar345 Format

One image consists of the following items:

Spiral Image Format

A spiral image consists of:

Mar345 Header

The image header consists of "lines" of 64 bytes each with exception of the first line, that contains 16 4-byte words (32 bit integers). The very first value always is 1234 for all scanning modes, i.e. it is just a marker for the necessity of byte swapping and does NOT give the size of the image (in contrast to the first value of the old image formats which is 1200 or 2000 or its byte swapped equivalent). Programs of the mar345 suite rely on this value to decide wether the image is in old format or in the new one and/or if byte-swapping is required. The remaining 15 32-bit integers are:
2) Size of image in one dimension
3) Number of high intensity pixels
4) Image format (1=COMPRESSED, 2=SPIRAL)
5) Collection mode (0=DOSE, 1=TIME)
6) Total number of pixels in image
7) Pixel length (in mm * 1.000)
8) Pixel height (in mm * 1.000)
9) Used wavelength (in Ang * 1.000.000 )
10) Used distance (in mm * 1.000 )
11) Used starting PHI (in deg. * 1.000 )
12) Used ending PHI (in deg. * 1.000 )
13) Used starting OMEGA (in deg. * 1.000 )
14) Used ending OMEGA (in deg. * 1.000 )
15) Used CHI (in deg. * 1.000 )
16) Used TWOTHETA (in deg. * 1.000 )

If the first value is not 1234, the bytes of the following 15 integers must be swapped.

The next 64 character line contains a general identifier string for this type of file: "mar research" (bytes 65 to 76 in the image file). This is for possible use with the "file" command under Unix.

All following lines contain keyworded information. The last keyword should be "END OF HEADER". All keywords are in capital letters and all "lines" are pure ASCII, so they are not affected by the byte order of different computer platforms. Processing of the keywords is not required. For using the formats correctly, the most important information is contained in the second (bytes 5-8) and third (bytes 9-12) header value: the size of the image and the number of high intensity pixels!

KEYWORDS in MAR345 HEADER

PROGRAM <program name> <version number>
Keyword PROGRAM always is the first in the list of keywords, i.e. at byte 128!
DATE <weekday month day hh:mm:ss year>
Date and time of production.
Example: DATE Tue Jul 9 13:06:05 1996
SCANNER <serial_number>
Serial number of the scanner.
Example: SCANNER 12
FORMAT <size> <type> <no_pixels>
<size> is the number of pixels in one dimension, <type> is "MAR345", "PCK345" or "SPIRAL" and <no_pixels> gives the total number of pixels in the image.
Example: FORMAT 1200 SPIRAL 1111647
HIGH <n_high>
Number of pixels with values > 65535 (16-bit). Depending on this value, programs should try to read <n_high> high intensity pixel pairs (address in array and 32-bit pixel value) preceding the 16-bit data array.
Example: HIGH 0
PIXEL LENGTH <pix_length> HEIGHT <pix_height>
Size of one pixel in micron units (1000. * mm). In SPIRAL format, length is shorter than height (double sampling).
Example: PIXEL LENGTH 75 HEIGHT 150
OFFSET ROFF <roff> TOFF <toff>
Radial and tangential offset of the scanner in mm (constants).
Example: OFFSET ROFF 0.1 TOFF -0.05
MULTIPLIER <fmul>
High intensity multiplier.
Example: MULTIPLIER 1.000
GAIN <gain>
Gain of the detector, i.e. the number of photons required to produce 1 ADC unit.
Example: GAIN 1.000
WAVELENGTH <wave>
Used wavelength in Angstroems.
Example: WAVELENGTH 0.7107
DISTANCE <distance>
Used distance crystal to detector in mm.
Example: DISTANCE 70.0
RESOLUTION <dmax>
Maximum resolution (Ang.) at edge of the plate.
Example: RESOLUTION 2.1
PHI START <phi_start> END <phi_end> OSC <n_osc>
PHI values at start and end of exposure. <n_osc> is the number of PHI oscillations during this exposure.
Example: PHI START 10.000 END 11.000 OSC 1
OMEGA START <omega_start> END <omega_end> OSC <n_osc>
OMEGA values at start and end of exposure. <n_osc> is the number of omega oscillations during this exposure.
Example: OMEGA START 0.000 END 0.000 OSC 0
CHI <chi>
CHI value during this exposure.
Example: CHI 90.0
TWOTHETA <twotheta>
2-theta value during this exposure.
Example: TWOTHETA 0.0
CENTER X <xcen> Y <ycen>
Coordinates of direct beam in pixel units.
Example: CENTER X 999.000 Y 1001.100
MODE <dcmode>
Mode of data collection: "TIME" or "DOSE".
Example: MODE TIME
TIME <exp_time>
Exposure time in seconds. In DOSE mode, the time varies depending to X-ray flux.
Example: TIME 60.00
COUNTS START <cnt_beg> END <cnt_end> MIN <cnt_min> MAX <cnt_max> AVE <cnt_ave> SIG <cnt_sig> NMEAS <cnt_n>
X-ray counts as measured by the second ionization chamber: minimum, maximum and average value, values at start and end of exposure and sigma of average reading. <cnt_n> is the number of times the X-ray intensity has actually been read during the exposure.
Example: COUNTS START 12.1 END 11.50 MIN 10.9 MAX 12.4 AVE 11.6 SIG 0.8 NMEAS 120
INTENSITY MIN <int_min> MAX <int_max> AVE <int_ave> SIG <int_sig>
Pixel values in image: minimum, maximum, average value and sigma.
Example: INTENSITY MIN 8 MAX 32987 AVE 432.4 SIG 25.9
HISTOGRAM START <his_beg> END <his_end> MAX <his_max>
Distribution of pixel values in image (used for distributing colours at display). <his_beg> and <his_end> give the limits for the range of intensities to distribute available colours. <his_max> is the most frequent pixel value in the image.
Example: HISTOGRAM START 120 END 640 MAX 216
GENERATOR <type> kV <kiloVolt> mA <milliAmps>
Type of x-ray source ("SEALED TUBE", "ROTATING ANODE" or "SYNCHROTRON") and power settings.
Example: GENERATOR SEALED TUBE kV 40.0 mA 50.0
MONOCHROMATOR <type> POLAR <polar>
Type of monochromator ("GRAPHITE", "MIRRORS" or "FILTER") and value of x-ray polarization.
Example: MONOCHROMATOR GRAPHITE POLAR 0.000
COLLIMATOR WIDTH <width> HEIGHT <height>
Aperture of horizontal (<width>) and vertical (<height>) slits in mm. These values are for the second of the two slit systems of the mar research collimation system. They determine the size of the beam.
Example: COLLIMATOR WIDTH 0.3 HEIGHT 0.3
REMARK <text>
Additional remark (one line only)
Example: REMARK Lysozyme crystal 0.5x0.8 mm

See Also

mar300_formats

Author

Claudio Klein, marXperts GmbH, Norderstedt, Germany

Copyright

© Copyright 2000-2004 marXperts GmbH, Norderstedt, Germany

Address

marXperts GmbHPhone: +49 - (40) - 529 884-0
Werkstr. 3 FAX: +49 - (40) - 529 884-20
D-22844 Norderstedt - GERMANYinfo@marXperts.com
www.marXperts.com

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