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J Digit Imaging
DOI 10.1007/s10278-013-9657-9
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Basic Concepts
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Pixel Depth
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Pixel depth is the number of bits used to encode the information of each pixel. Every image is stored in a file and kept in
the memory of a computer as group of bytes. Bytes are group
of 8 bits and represent the smallest quantity that can be stored
in the memory of a computer. This means that if a 256 by 256
pixels image has a pixel depth of 12 or 16 bits, the computer
will always store two bytes per pixel and then the pixel data
will require 2562562=131,072 bytes of memory in both
cases. With a pixel depth of 2 bytes per pixels, it is possible to
codify and store integer numbers between 0 and 65,535
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Introduction
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M. Larobina (*)
Istituto di Biostrutture e Bioimmagini, Consiglio Nazionale delle
Ricerche, Via Tommaso De Amicis, 95, 80145 Naples, Italy
e-mail: michele.larobina@cnr.it
L. Murino
Istituto per le Applicazioni del Calcolo, CNR, Naples, Italy
AUTHOR'S PROOF
J Digit Imaging
Photometric Interpretation
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Metadata
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Pixel Data
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This is the section where the numerical values of the pixels are
stored. According to the data type, pixel data are stored as
integers or floating-point numbers using the minimum number of bytes required to represent the values (see Table 1).
Looking at images generated by tomographic imaging modalities, and sent to a Picture Archiving and Communication
System (PACS) or a reading station, radiological images like
CT and MR and also modern nuclear medicine modalities, like
PET and SPECT, store 16 bits for each pixel as integers.
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three samples per pixel are stored. The images will have a
pixel depth of 24 bits and are said to be in true color.
Color is for example used to encode blood flow direction
(and velocity) in Doppler ultrasound to show additional functional information onto a gray scale anatomical image as
colored overlays, as in the case of fMRI activation sites, to
simultaneously display functional and anatomical images as in
the PET/CT or PET/MRI, and sometimes in place of gray
tones to highlight signal differences.
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(2161); alternatively, it is possible to represent integer numbers between 32,768 and +32,767 using 15 bits to represent
the numbers and 1 bit to represent the sign. Image data may
also be real numbers. The Institute of Electrical and Electronics Engineers created a standard (IEEE-754) in which defines
two basic formats for the encoding in binary of floating-point
numbers: the single precision 32-bit and the double precision
64-bit. The standard addresses the problem of the precision
with which a finite number of combination obtainable with a
sequence of n-bit (2n 1) can represent a continuous range of
real numbers. Although unusual, pixels can store complex
numbers. Complex data have a real and an imaginary component which are referred as pairs of real numbers. Therefore,
complex data typically have a pixel depth twice that used to
represent a single real number.
From the previous overview emerges that the pixel
depth is a concept related to the memory space necessary
to represent in binary the amount of information we want
to store in a pixel.
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AUTHOR'S PROOF
J Digit Imaging
t1:1
t1:2
Format
Header
Extension
Data types
t1:3
Analyze
t1:4
Nifti
.nii
Minc
.mnc
Dicom
.dcm
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t1:6
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File Formats
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AUTHOR'S PROOF
J Digit Imaging
Analyze
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Nifti
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Minc
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The Minc file format was developed at the Montreal Neurological Institute (MNI) starting from 1992 to provide a flexible
data format for medical imaging. The first version of Minc
format (Minc1) was based on the standard Network Common
Data Format (NetCDF). Subsequently, to overcame the limit
in supporting large data files and to provide other new features, the Minc development team chose to switch from
NetCDF to Hierarchical Data Format version 5 (HDF5). This
new release, not compatible with the previous one, was
called Minc2. The format is mainly used by software
tools developed by the MNI Brain Imaging Center, i.e.,
a viewer and a processing software library [7]. A set of
utilities which allow the conversion to and from Dicom
and Nifti formats, and between Minc1 and Minc2 have
been made available by the same group.
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pixel data are merged. The header has a size of 348 bytes in the
case of .hdr and .img data storage, and a size of 352 bytes in
the case of a single .nii file for the presence of four additional
bytes at the end, essentially to make the size a multiple of 16,
and also to provide a way to store additional-metadata, in which
case these 4 bytes are nonzero. A practical implementation of an
extended Nifti format for the processing of diffusion-weighted
magnetic resonance data is described in [9].
The Nifti format allows a double way to store the orientation of the image volume in the space. The first, comprising a
rotation plus a translation, to be used to map voxel coordinates
to the scanner frame of reference; this rigid body transformation is encoded using a quaternion [10]. The second
method is used to save the 12 parameters of a more general
linear transformation which defines the alignment of the image volume to a standard or template-based coordinate system. This spatial normalization task is common in brain functional image analysis [11].
The Nifti format has rapidly replaced the Analyze in neuroimaging research, being adopted as the default format by
some of the most widespread public domain software packages, as, FSL [12], SPM [13], and AFNI [14]. The format is
supported by many viewers and image analysis software like
3D Slicer [15], ImageJ [16], and OsiriX, as well as other
emerging software like R [17] and Nibabel [18], besides
various conversion utilities.
An update version of the standard, the Nifti-2, developed to
manage larger data set has been defined in the 2011. This new
version encode each of the dimensions of an image matrix
with a 64-bit integer instead of a 16-bit as in the Nifti-1,
eliminating the restriction of having a size limit of 32,767.
This updated version maintains almost all the characteristics
of the Nifti-1 but, as reserve for some header fields the double
precision, comes with a header of 544 bytes [19].
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the Interfile format [8]. It was created in the 1980s and has
been used for many years for the exchange of nuclear medicine images. An Interfile image consists of a pair of files, one
containing metadata information in ASCII format, that the
standard calls administrative information, and one containing
the image data. The Interfile header can be viewed and edited
with a normal text editor.
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AUTHOR'S PROOF
J Digit Imaging
Dicom
Discussion
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AUTHOR'S PROOF
J Digit Imaging
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Conclusion
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The field of image file formats is constantly evolving. Regarding the encoding of images generated by diagnostic modalities, Dicom is the preferred standard and it will be for many
years to come thanks to a great flexibility to follow the
technological development and medical imaging advances
and the integration with a network infrastructure. On the other
hand, in the near future, we will probably see the proposal and
the adoption of new file formats for the post-processing, even
if the idea that these formats are a convenient way to only
retain essential information will lose strength. The weight of
image-specific and image-related information is growing in
the world of image processing, and the potential integration of
results obtained by quantitative analysis in a clinical context is
an open issue.
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References
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AUTHOR'S PROOF
J Digit Imaging
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