Medical Imaging
Informatics
Dr. Jun Ni, Associate Professor
Department of Radiology
Carver College of Medicine
The University of Iowa
Medical Image Format
Image File Format
Defined as the standardized means of organizing
and storing digital images.
Image files are composed of either pixel or vector
(geometric) data that are rasterized to pixels in
graphic display (such as monitor, print and other
devices).
Medical Image Format
Image File Format
The pixels that constitute an image are ordered as a
grid (columns and rows); each pixel has magnitudes
of brightness (expressed by gray-scale value) and
color.
Medical Image Format
Image File Format
Name (identifier)
File size
Determined based on image dimension size, the number
of bytes
increases with the number of pixels composing an image
(dimensions), and the color depth of the pixels.
The greater the number of rows and columns, the greater
the image resolution, and the larger the file.
Medical Image Format
Image File Format
Name (identifier)
File size
Also, each pixel of an image increases in size when its
color depth increasesan 8-bit pixel (1 byte) stores 256
colors, a 24-bit pixel (3 bytes) stores 16 million colors,
more (close to truecolor)
Same for gray-scale, large the gray scale levels (determined
by bits number), the larger image size
Medical Image Format
Image File Format
Compression
Image file size is also determined by the compression
method associated with the file format
Medical Image Format
Image File Format
image file type and formats
Hundreds of types
The PNG, JPEG, and GIF formats are most often used
to display images on the Internet.
Classified into the two three families of graphics:
Raster
Vector
Metafile
Combined with raster and vector information
Medical Image Format
Raster Graphic Format
These formats store images as bitmaps (also called as
pixmaps).
JPEG/JFIF
Medical Image Format
JPEG (Joint Photographic Experts Group) is a
compression method; JPEG-compressed images
are usually stored in the JFIF (JPEG File
Interchange Format) file format.
JPEG compression is (in most cases) lossy
compression.
The JPEG/JFIF filename extension in DOS is
JPG (other operating systems may use JPEG).
Medical Image Format
Nearly every digital camera can save images in
the JPEG/JFIF format, which supports 8 bits
per color (red, green, blue) for a 24-bit total,
producing relatively small files.
When not too great, the compression does not
noticeably detract from the image's quality; but
JPEG files suffer generational degradation when
repeatedly edited and saved.
Medical Image Format
The compression methods used are different from
the ones in standard JFIF/JPEG; they improve
quality and compression ratios, but also require
more computational power to process.
Medical Image Format
JPEG 2000
is a compression standard enabling both lossless and
lossy storage.
JPEG 2000 also adds features that are missing in
JPEG.
It is not nearly as common as JPEG, but it is used
currently in professional movie editing and
distribution (e.g., some digital cinemas use JPEG
2000 for individual movie frames).
Medical Image Format
TIFF (Tagged Image File Format)
is a flexible format that normally saves 8 bits or 16
bits per color (red, green, blue) for 24-bit and 48-bit
totals, respectively, usually using either the TIFF or
TIF filename extension.
Medical Image Format
GIF (Graphics Interchange Format)
limited to an 8-bit palette, or 256 colors.
This makes the GIF format suitable for storing
graphics with relatively few colors such as simple
diagrams, shapes, logos and cartoon style images.
Medical Image Format
GIF (Graphics Interchange Format)
The GIF format supports animation and is still
widely used to provide image animation effects.
It also uses a lossless compression that is more
effective when large areas have a single color, and
ineffective for detailed images.
Extension name is GIF
Medical Image Format
BMP file format (Windows bitmap) handles
graphics files within the Microsoft Windows OS.
Typically, BMP files are uncompressed, hence they
are large; the advantage is their simplicity and wide
acceptance in Windows programs.
Original (color)
Original (Gray-scale)
BMP Lenna
Medical Image Format
PNG (Portable Network Graphics)
PNG is robust, providing both full file integrity
checking and simple detection of common
transmission errors.
Also, PNG can store gamma and chromaticity data
for improved color matching on heterogeneous
platforms.
Medical Image Format
PNG (Portable Network Graphics)
Some programs do not handle PNG gamma
correctly, which can cause the images to be saved or
displayed darker than they should be.
Medical Image Format
Advantages
The PNG file format supports true color (16 million
colors) while the GIF supports only 256 colors.
The PNG file excels when the image has large,
uniformly colored areas.
The lossless PNG format is best suited for editing
pictures, and the lossy formats, like JPG, are best for
the final distribution of photographic images,
because in this case JPG files are usually smaller than
PNG files.
Medical Image Format
Advantages
All contemporary web browsers now support all
common uses of the PNG format
PNG provides a patent-free replacement for GIF
and can also replace many common uses of TIFF.
Medical Image Format
Advantages
Indexed-color, grayscale, and truecolor images are
supported, plus an optional alpha channel.
PNG is designed to work well in online viewing
applications, such as the World Wide Web, so it is
fully streamable with a progressive display option
Medical Image Format
RAW (Raw Image Formats)
Usually use a lossless or nearly-lossless compression,
and produce file sizes much smaller than the TIFF
formats of full-size processed images from the same
cameras.
Although there is a standard raw image format, (ISO
12234-2, TIFF/EP), the raw formats used by most
cameras are not standardized or documented, and
differ among camera manufacturers.
Medical Image Format
RAW (Raw Image Formats)
Raw files are so named because they are not yet
processed and therefore are not ready to be printed
or edited with a bitmap graphics editor.
Raw image files are sometimes called digital
negatives, as they fulfill the same role as negatives
in film photography: that is, the negative is not
directly usable as an image, but has all of the
information needed to create an image.
Medical Image Format
RAW (Raw Image Formats)
The image is processed by a raw converter to a
"positive" file format such as TIFF or JPEG for
storage, printing, or further manipulation, which
often encodes the image in a device-dependent
colorspace.
Medical Image Format
RAW (Raw Image Formats)
Likewise, the process of converting a raw image file
into a viewable format is sometimes called
developing a raw image, by analogy with the film
development process used to convert photographic
film into viewable prints.
Medical Image Format
RAW (Raw Image Formats)
Many raw file formats (including 3FR (Hasselblad),
DCR, K25, KDC (Kodak), CR2 (Canon), ERF
(Epson), MEF (Mamiya), MOS (Leaf), NEF
(Nikon), ORF (Olympus), PEF (Pentax), RW2
(Panasonic) and ARW, SRF, SR2 (Sony)) are based
on the TIFF file format.
These files may deviate from the TIFF standard in a
number of ways, including the use of a non-standard
file header, the inclusion of additional image tags and
the encryption of some of the tagged data.
Medical Image Format
RAW (Raw Image Formats) that are options
available on some digital cameras.
Many medical modality and devices still use RAW
data format.
The applications of using RAW data format are still
active.
Medical Image Format
RAW (Raw Image Formats) -- MetaFile
Another raw data format is cataloged to Metafile
Metafile is a generic term for a file format that can
store multiple types of data. This commonly includes
graphics file formats.
These graphics files can contain raster, vector, and
type data. A common use for these files is to provide
support for an operating system's computer
graphics. Microsoft Windows uses Windows
Metafile, Mac OS X uses PDF, and X11 uses
Medical Image Format
RAW (Raw Image Formats)
In addition to straight image formats, Metafile
formats are portable formats which can include both
raster and vector information.
Most PC applications open metafiles and then save
them in their own native format.
Page description language refers to formats used to
describe the layout of a printed page containing text,
objects and images. Examples are PostScript, PDF
and PCL.
Medical Image Format
DICOM Digital Imaging and Communications
in Medicine
A standard for handling, storing, printing, and
transmitting information in medical imaging.
It includes not only a file format definition, but also
a network communications protocol.
Medical Image Format
DICOM Digital Imaging and Communications
in Medicine
The communication protocol is an application
protocol that uses TCP/IP to communicate between
systems.
DICOM files can be exchanged between two entities
that are capable of receiving image and patient data
in DICOM format.
Medical Image Format
DICOM Digital Imaging and Communications
in Medicine
The National Electrical Manufacturers Association
(NEMA) holds the copyright to this standard. It was
developed by the DICOM Standards Committee
DICOM enables the integration of scanners, servers,
workstations, printers, and network hardware from
multiple manufacturers into a picture archiving and
communication system (PACS).
Medical Image Format
DICOM Digital Imaging and Communications
in Medicine
The different devices (medical image modalities)
come with DICOM conformance statements which
clearly state the DICOM classes they support.
DICOM has been widely adopted by hospitals and is
making inroads in smaller applications like dentists'
and doctors' offices.
Medical Image Format
DICOM Digital Imaging and Communications
in Medicine
DICOM is kind of metadata data format contains
structure which allows to have not only image
information, but also other patient information and
medical identification
Medical Image Format
DICOM Digital Imaging and Communications
in Medicine
A DICOM data object consists of a number of
attributes, including items such as name, ID, etc.,
and also one special attribute containing the image
pixel data (i.e. logically, the main object has no
"header" as such - merely a list of attributes,
including the pixel data).
Medical Image Format
DICOM Digital Imaging and Communications
in Medicine
A single DICOM object can only contain one
attribute containing pixel data.
For many modalities, this corresponds to a single
image. One of advantages is the DICOM attribute
may contain multiple "frames", allowing storage of
cine loops or other multi-frame data.
Medical Image Format
DICOM Digital Imaging and Communications
in Medicine
Another example is multi-dimensional multi-frame
image. In these cases three- or four-dimensional data
can be encapsulated in a single DICOM object.
Pixel data can be compressed using a variety of
standards, including JPEG, JPEG Lossless, JPEG
2000.
Medical Image Format
DICOM Digital Imaging and Communications
in Medicine
Each DICOM object has
Data Object and Services Object
Medical Image Format
DICOM service objects
Store
Storage Commitment
Query/Retrieve
Modality Worklist
Modality Performed Procedure Step
Printing
DICOM Format
DICOM Data Structure Encodes (value
representation code)
Value Representation
Description
AE
Application Entity
AS
Age String
AT
Attribute Tag
CS
Code String
DA
Date
DS
Decimal String
DT
Date/Time
FL
Floating Point Single (4 bytes)
FD
Floating Point Double (8 bytes)
IS
Integer String
LO
Long String
LT
Long Text
OB
Other Byte
OF
Other Float
OW
Other Word
PN
Person Name
SH
Short String
SL
Signed Long
SQ
Sequence of Items
SS
Signed Short
ST
Short Text
TM
Time
UI
Unique Identifier
UL
Unsigned Long
UN
Unknown
US
Unsigned Short
UT
Unlimited Text
Modality
Description
BI
CD
CR
CT
DD
DG
DX
EC
EM
ES
GM
LS
MA
MG
MR
MS
NM
OT
PT
RF
RG
RT
SC
SM
ST
TG
US
VL
XA
Modality of
Modality of
Modality of
Modality of
Modality of
Modality of
Modality of
Modality of
Modality of
Modality of
Modality of
Modality of
Modality of
Modality of
Modality of
Modality of
Modality of
Modality of
Modality of
Modality of
Modality of
Modality of
Modality of
Modality of
Modality of
Modality of
Modality of
Modality of
Modality of
type Biomagnetic Imaging
type Color Flow Doppler-Retired 2008
type Computed Radiography
type Computed Tomography
type Duplex Doppler-Retired 2008
type Diaphanography
type Digital Radiography
type Echo cardiography - Retired
type Electron Microscope
type Endoscopy
type General Microscopy
type Laser Surface Scan
type Magnetic Resonance Angiography - Retired
type Mammography
type Magnetic Resonance
type Magnetic Resonance Spectroscopy - Retired
type Nuclear Medicine
type Other
type Positron Emission Tomography
type Radio Fluoroscopy
type Radiographic Imaging (conventional film screen)
type Radiation Therapy
type Secondary Capture
type Slide Microscopy
type Single-Photon Emission Computed Tomography - Retired 2008
type Thermography
type Ultra Sound
type Visible Light
type X-Ray Angiography
XC
Modality of type External Camera (Photography)
DICOM Format
DICOM standard port numbers:
104 well-known port for DICOM over TCP or
UDP; many operating systems require special
privileges to use it.
2761 registered port for DICOM using Integrated
Secure Communication Layer (ISCL) over TCP or
UDP
DICOM Format
DICOM standard port numbers:
2762 registered port for DICOM using Transport
Layer Security (TLS) over TCP or UDP
11112 registered port for DICOM using standard,
open communication over TCP or UDP
DICOM Format
Further reading
Book recommended:
Oleg S. Pianykh, Digital Imaging and Communications in
Medicine (DICOM), Springer, 2008
Steven C. Horii, A nontechnical Introduction to DICOM,
RSNA
DICOM documentations (link)
Introduction to DICOM (link)
DICOM Wiki page (link)
DICOM Format
References:
DICOM Home Page: http://medical.nema.org/
The latest DICOM specification
DICOM Standard Status (approved and proposed changes)
Brief introduction to DICOM
Introduction to DICOM using OsiriX
Medical Image FAQ part 2 - Standard formats including
DICOM.
Medical Image FAQ part 8 - Contains a long list DICOM
software.
Collection of DICOM images (clinical images and technical
testpatterns)
