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mar_images - description of image formats for images collected on a
mar research Imaging Plate Detector System.
mar research scanners
produce the following image file formats:
Standard image consists of a number of records of
fixed size. The actual size of each record depends on the scanning mode:
small images (1200x1200 pixels) use 2400 byte records, big images (2000x2000
pixels) use 4000 byte records. One image consists of the following records
- spiral images:
- 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.
- standard mar research ".image" files:
and corrected uncompressed images. Required disk space is approx. 2.3 MB for
an image of 1200x1200 pixels and 8.1 MB for an image of 2000x2000 pixels.
- compressed mar research ".pck" files:
- Transformed and corrected compressed
images. The compression algorithm was kindly provided by Dr. J.P. Abrahams
of the LMB in Cambridge, GB. Required disk space is approx. 0.8 MB for an
image of 1200x1200 pixels and 2.9 MB for an image of 2000x2000 pixels.
- Record 1: header.
- Records 2-1201 (or 2-2001): An image data array of 1200
(or 2000) records with 1200 (or 2000) pixels each. All pixels values are
16-bit unsigned integers with values ranging from 0 to 65535.
- Record 1202
(or 2002)-...: An array of addresses and values of pixels whose values are
larger than 65535. The pixel address is a number corresponding to the
linear array starting at pixel 1 and ending at pixel 1.440.000 (or 4.000.000).
One "high intensity" record thus consists of up to 600 (1000) value pairs
(address+intensity). In the 16-bit array the value corresponding to the
high intensity pixel is set to 65535. The value in the high intensity record
replaces the value in the 16-bit array.
The number of pixels with values
larger than 65535 is included in the image header record. All image reading
routines will try to read the corresponding number of high intensity records
if the number in the image header unequals zero.
Compressed "pck" image have the following structure:
A spiral image consists of:
- Record 1:
header = 2400 or 4000 bytes.
- Record 2... High intensity pixels (if present
at all, see above) = 2400 or 4000 bytes each.
- Optional high intensity records
are followed by a compressed byte array with 1200x1200 (or 2000x2000) image
data. The compressed array contains exactly the same information as the
16-bit image array of the standard image files, but needs approx. 70% less
The image header contains the
following entries: 10 32-bit integers, 15 32-bit floats, and a 24 byte string.
- A header record. Length
is 2048 bytes.
- An image data array consisting of records. Each record consists
of 1024 pixel values (16-bit unsigned integers), i.e 2048 bytes. Small images
(1200x1200 pixels) have 4352 spiral records, big images (2000x2000 pixels)
have 11952 spiral records. The header structure is the same as the one for
the transformed images but inbetween the "scanning date" entry and the
29 16-byte strings there are 6 additional 32 bit integers that contain information
required for transformation.
The 32-bit integers are:
- Number of pixels in x: 1200 or 2000
- Number of
pixels in y: 1200 or 2000
- Record length in byte: 2400 or 4000
- Max. no. of
records: 1200 or 4000
- No. of high intensity pixels in image.
- No. of high intensity
records in image.
- No. of X-ray counts at start of exposure.
- No. of X-ray counts
at end of exposure.
- Exposure time in seconds.
- Exposure dose in units.
32-bit floats are:
- Sum of X-ray counts.
- Maximum radius.
- Minimum radius.
- Centre in x.
- Centre in y.
- Used wavelength.
- Used distance
- PHI axis at start of exposure.
- PHI axis at end of exposure.
- OMEGA axis position.
- High intensity multiplier.
The 24-byte string is:
In spiral images the scanning date is followed by 6 more 32-bit integer
If images have been produced using the marControl data collection
software, 29 strings follow, each one consisting of 16 bytes (characters).
The first 4 strings are:
marControl, marView, marTools, marxform
- Identification string: "MARCONTROL V1.0"
serial number: "049" or similars.
- Computer architecture: "SGI", "VMS/VAX"
- Sum of X-ray counts during one exposure.
- Entries 5-29 are just
repeats of the corresponding values of 10 integers and 15 floats as character
strings. The advantage of using strings is that bytes of these strings do
not need to be swapped when images are transferred between computer architectures.
marXperts GmbH, Norderstedt, Germany
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GmbH, Norderstedt, Germany
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