DICOM PS3.3 2019d - Information Object Definitions

C.8.12.4 Whole Slide Microscopy Image Module

Table C.8.12.4-1 specifies the Attributes that describe the Whole Slide Microscopy Image Module.

Table C.8.12.4-1. Whole Slide Microscopy Image Module Attributes

Attribute Name

Tag

Type

Attribute Description

Image Type

(0008,0008)

1

Image identification characteristics.

See Section C.8.12.4.1.1 for specialization.

Imaged Volume Width

(0048,0001)

1

Width of total imaged volume (distance in the direction of rows in each frame) in mm. See Section C.8.12.4.1.2

Imaged Volume Height

(0048,0002)

1

Height of total imaged volume (distance in the direction of columns in each frame) in mm. See Section C.8.12.4.1.2

Imaged Volume Depth

(0048,0003)

1

Depth of total imaged volume (distance in the Z direction of focal planes) in µm. See Section C.8.12.4.1.2

Total Pixel Matrix Columns

(0048,0006)

1

Total number of columns in pixel matrix; i.e., width of total imaged volume in pixels. See Section C.8.12.4.1.3

Total Pixel Matrix Rows

(0048,0007)

1

Total number of rows in pixel matrix; i.e., height of total imaged volume in pixels. See Section C.8.12.4.1.3

Total Pixel Matrix Focal Planes

(0048,0303)

1C

Total number of focal planes (Z locations) in the pixel matrix; i.e., depth of total imaged volume in pixels. See Section C.8.12.4.1.3

Required if Dimension Organization Type (0020,9311) is present with a value of TILED_FULL. May be present otherwise.

Note

Total Pixel Matrix Focal Planes (0048,0303) describes the number of focal planes separately encoded, and is distinct from Number of Focal Planes (0048,0013), which describes in what manner different focal planes were combined into a single encoded plane (focus stacking).

Total Pixel Matrix Origin Sequence

(0048,0008)

1

Location of pixel 1\1 of the total pixel matrix in the Slide Coordinate System Frame of Reference.

Only a single Item shall be included in this Sequence.

See Section C.8.12.4.1.4 and Section C.8.12.2.1.1 for further explanation

>X Offset in Slide Coordinate System

(0040,072A)

1

The X offset in millimeters from the Origin of the Slide Coordinate System.

>Y Offset in Slide Coordinate System

(0040,073A)

1

The Y offset in millimeters from the Origin of the Slide Coordinate System.

Image Orientation (Slide)

(0048,0102)

1

The direction cosines of the first row and the first column of the total pixel matrix with respect to the Slide Coordinate System Frame of Reference. See Section C.8.12.4.1.4

Samples Per Pixel

(0028,0002)

1

Number of samples (color planes) per frame in this image.

Enumerated Values:

3

1

See Section C.8.12.4.1.5 for further explanation.

Photometric Interpretation

(0028,0004)

1

Specifies the intended interpretation of the pixel data.

See Section C.8.12.4.1.5 for Enumerated Values.

Planar Configuration

(0028,0006)

1C

Indicates whether the pixel data are encoded color-by-plane or color-by-pixel. Required if Samples per Pixel (0028,0002) has a value greater than 1.

Enumerated Values:

0

color-by-pixel

Number of Frames

(0028,0008)

1

Number of frames in a multi-frame image.

Enumerated Values if Image Type (0008,0008) Value 3 is LOCALIZER or LABEL:

1

Bits Allocated

(0028,0100)

1

Number of bits allocated for each pixel sample.

Enumerated Values:

8

16

Bits Stored

(0028,0101)

1

Number of bits stored for each pixel sample. Shall be equal to Bits Allocated (0028,0100).

High Bit

(0028,0102)

1

Most significant bit for pixel sample data. High Bit (0028,0102) shall be one less than Bits Stored (0028,0101).

Pixel Representation

(0028,0103)

1

Data representation of pixel samples.

Enumerated Values:

0

unsigned integer

Acquisition DateTime

(0008,002A)

1

The date and time that the acquisition of data that resulted in this image started.

Acquisition Duration

(0018,9073)

3

Duration of the image acquisition in seconds.

Lossy Image Compression

(0028,2110)

1

Specifies whether an Image has undergone lossy compression (at a point in its lifetime).

Enumerated Values:

00

Image has NOT been subjected to lossy compression.

01

Image has been subjected to lossy compression.

Once this value has been set to 01 it shall not be reset.

See Section C.7.6.1.1.5

Lossy Image Compression Ratio

(0028,2112)

1C

Describes the approximate lossy compression ratio(s) that have been applied to this image.

See Section C.7.6.1.1.5.2.

Required if Lossy Image Compression (0028,2110) is "01".

Lossy Image Compression Method

(0028,2114)

1C

A label for the lossy compression method(s) that have been applied to this image.

See Section C.7.6.1.1.5.1.

Required if Lossy Image Compression (0028,2110) is "01".

Presentation LUT Shape

(2050,0020)

1C

Specifies an identity transformation for the Presentation LUT, such that the output of all grayscale transformations defined in the IOD containing this Module are defined to be P-Values.

Enumerated Values:

IDENTITY

output is in P-Values.

Required if Photometric Interpretation (0028,0004) is MONOCHROME2.

Rescale Intercept

(0028,1052)

1C

The value b in relationship between stored values (SV) and the output units.

Output units = m*SV + b.

Required if Photometric Interpretation (0028,0004) is MONOCHROME2.

Enumerated Values:

0

Rescale Slope

(0028,1053)

1C

m in the equation specified by Rescale Intercept (0028,1052).

Required if Photometric Interpretation (0028,0004) is MONOCHROME2.

Enumerated Values:

1

Volumetric Properties

(0008,9206)

1

Indication if geometric manipulations are possible with frames in the SOP Instance. See Section C.8.16.2.1.2.

Enumerated Values:

VOLUME

pixels represent the volume specified for the image, and may be geometrically manipulated

Specimen Label in Image

(0048,0010)

1

Indicates whether the specimen label is captured in the image.

Enumerated Values:

YES

NO

Burned In Annotation

(0028,0301)

1

Indicates whether or not image contains sufficient burned in annotation to identify the patient.

Enumerated Values:

YES

NO

Note

If Specimen Label in Image (0048,0010) value is YES, Burned In Annotation (0028,0301) might be NO if the label includes only a specimen identifier and not patient identifying data.

Focus Method

(0048,0011)

1

Method of focusing image

Enumerated Values:

AUTO

autofocus

MANUAL

includes any human adjustment or verification of autofocus

Extended Depth of Field

(0048,0012)

1

Image pixels were created through combining of image acquisition at multiple focal planes (focus stacking).

Enumerated Values:

YES

NO

Number of Focal Planes

(0048,0013)

1C

Number of acquisition focal planes used for extended depth of field.

Required if Extended Depth of Field (0048,0012) value is YES

Note

Total Pixel Matrix Focal Planes (0048,0303) describes the number of focal planes separately encoded, and is distinct from Number of Focal Planes (0048,0013), which describes in what manner different focal planes were combined into a single encoded plane (focus stacking).

Distance Between Focal Planes

(0048,0014)

1C

Distance between acquisition focal planes used for extended depth of field, in µm.

Required if Extended Depth of Field (0048,0012) value is YES.

Note

Spacing Between Slices (0018,0088) describes the spacing of focal planes separately encoded, and is distinct from Distance Between Focal Planes (0048,0014), which describes in what manner different focal planes were combined into a single encoded plane (focus stacking).

Acquisition Device Processing Description

(0018,1400)

3

Description of visual processing performed on the image prior to exchange. Examples of this processing are: edge enhanced, gamma corrected, convolved (spatially filtered)

Convolution Kernel

(0018,1210)

3

Label for convolution kernel used in acquisition device visual processing

Recommended Absent Pixel CIELab Value

(0048,0015)

3

A color value with which it is recommended to display the pixels of the Total Pixel Matrix that are not encoded. The units are specified in PCS-Values, and the value is encoded as CIELab. See Section C.10.7.1.1.


C.8.12.4.1 Whole Slide Microscopy Image Attribute Descriptions
C.8.12.4.1.1 Image Type

Image Type (0008,0008) is specified to be Type 1 with the following constraints:

Value 1 shall have a value of ORIGINAL or DERIVED

Value 2 shall have a value of PRIMARY

Value 3 (Image Flavor) shall have the Defined Terms in Table C.8.12.4-2.

Table C.8.12.4-2. Whole Slide Microscopy Image Flavors

LOCALIZER

Collected for the purpose of planning or navigating other images; provides frame-level navigational features.

VOLUME

Set of frames that define a regularly sampled volume

LABEL

Purpose of image is to capture the slide label only; non-label area shall not be present; the label is shown in Figure C.8-16.

OVERVIEW

Purpose of image is to provide an overview of the entire glass slide; shall include the label, the specimen and the empty space that are shown in Figure C.8-16.

Note

One purpose of the OVERVIEW image is to allow visual quality control to assure that tissue fragments have not been omitted when selecting areas (manually or automatically) to digitize at high resolution. The OVERVIEW image is distinct from the lowest resolution VOLUME image(s) of WSI pyramids.


Value 4 (Derived Pixel) shall have the Defined Terms specified in Table C.8.12.4-3.

Table C.8.12.4-3. Whole Slide Microscopy Image Derived Pixels

NONE

No derivation of pixels (original)

RESAMPLED

Pixels were derived by down sampling a higher resolution image


No additional values shall be present.

C.8.12.4.1.2 Imaged Volume Width, Height, Depth

The full physical extent of the whole slide image target volume is described in the Attributes Imaged Volume Width (0048,0001), Imaged Volume Height (0048,0002), and Imaged Volume Depth (0048,0003). These values reflect the maximum extent in these dimensions. There is no requirement that this entire extent is actually encoded in frames of the Image SOP Instance, unless Dimension Organization Type (0020,9311) is present with a value of TILED_FULL.

The value of Imaged Volume Depth (0048,0003) shall not be 0. If only a single focal plane is imaged, the Imaged Volume Depth may be the optical depth of field as encoded in Slice Thickness (0018,0050) of the Pixel Measures Functional Group (see Section C.7.6.16.2.1).

C.8.12.4.1.3 Total Pixel Matrix Columns, Rows, Focal Planes

Total Pixel Matrix Columns (0048,0006), Total Pixel Matrix Rows (0048,0007) and Total Pixel Matrix Focal Planes (0048,0303) describe the size of the entire imaged volume as a single extent across all frames (tiles).

The extent would be as described in these Attributes if the whole volume would be imaged and encoded as a non-sparse pixel matrix with the pixel spacing as specified in Pixel Spacing (0028,0030) of the Pixel Measures Functional Group (see Section C.7.6.16.2.1), such as when Dimension Organization Type (0020,9311) is present with a value of TILED_FULL.

C.8.12.4.1.4 Total Pixel Matrix Origin Sequence and Image Orientation (Slide)

Total Pixel Matrix Origin Sequence (0048,0008) specifies the location of the top leftmost pixel of the pixel matrix, and Image Orientation (Slide) (0048,0102) specifies the direction cosines of the first row and the first column of the pixel matrix, both with respect to the Slide Coordinate System Frame of Reference (see Section C.8.12.2). Although the image acquisition may vary the true row and column orientation at the pixel scale to account for local variation in the physical specimen, this Attribute describes the orientation as if the Pixel Matrix were flat.

Note

Typically, Image Orientation (Slide) will describe only a planar rotation, as the image plane is usually nominally parallel to the slide surface.

C.8.12.4.1.5 Photometric Interpretation and Samples Per Pixel

See Section C.7.6.3.1.2.

Enumerated Values for Photometric Interpretation (0028,0004):

MONOCHROME2

RGB

YBR_FULL_422

YBR_ICT

YBR_RCT

The value shall be appropriate to the compression Transfer Syntax used, if any, and shall be MONOCHROME2 or RGB for uncompressed or lossless compressed Transfer Syntaxes that do not have defined color space transformations, YBR_ICT or RGB for irreversible JPEG 2000 Transfer Syntaxes, YBR_RCT or RGB for reversible JPEG 2000 Transfer Syntaxes, and YBR_FULL_422 or RGB for JPEG lossy compressed Transfer Syntaxes.

Note

  1. Future lossless and lossy Transfer Syntaxes may lead to the need for new definitions and choices for Photometric Interpretation. The Enumerated Values may therefore be extended with additional Photometric Interpretation values directly associated with new Transfer Syntaxes that are negotiated, and hence do not render existing implementations non-conformant.

  2. Motion compression Transfer Syntaxes are not expected to be used for Whole Slide Imaging, so the use of YBR_PARTIAL_420 for MPEG2, MPEG-4 AVC/H.264 and HEVC/H.265 Transfer Syntaxes is not permitted.

  3. The use of RGB with JPEG and JPEG 2000 is only intended to allow for conversion to DICOM of images from proprietary formats for which no color transformation from RGB to YBR was performed and the encoded components really are RGB. The value of Photometric Interpretation (0028,0004) describes what is actually encoded, so a value of RGB is not used when the compressed components are actually YBR.

Multi-spectral images may be encoded as a single wavelength band (color) in each frame using MONOCHROME2, or with up to three bands in each frame using one of the color Photometric Interpretations.

Enumerated Values for Samples per Pixel (0028,0002) when Photometric Interpretation (0028,0004) is MONOCHROME2:

1

Enumerated Values for Samples per Pixel (0028,0002) when Photometric Interpretation (0028,0004) is not MONOCHROME2:

3

DICOM PS3.3 2019d - Information Object Definitions