C.8.12 VL Modules and Functional Group Macros

C.8.12.1 VL Image Module

Table C.8-77 specifies the Attributes that describe a VL Image produced by Endoscopy (ES), General Microscopy (GM), Automated-Stage Microscopy (SM), External-camera Photography (XC), or other VL imaging Modalities.

Table C.8-77VL IMAGE MODULE ATTRIBUTES

Attribute Name Tag Type Attribute Description
Image Type (0008,0008) 1 Image identification characteristics. See C.8.12.1.1.6 for specialization.
Photometric Interpretation (0028,0004) 1 Specifies the intended interpretation of the pixel data. See C.8.12.1.1.1 for specialization of this Attribute.
Bits Allocated (0028,0100) 1 Number of bits allocated for each pixel sample. Each sample shall have the same number of bits allocated. See C.8.12.1.1.2 for specialization of this Attribute. See PS 3.5 for further explanation.
Bits Stored (0028,0101) 1 Number of bits stored for each pixel sample. Each sample shall have the same number of bits stored. See C.8.12.1.1.2 for specialization of this Attribute. See PS 3.5 for further explanation.
High Bit (0028,0102) 1 Most significant bit for pixel sample data. Each sample shall have the same high bit. See C.8.12.1.1.2 for specialization of this Attribute. See PS 3.5 for further explanation.
Pixel Representation (0028,0103) 1 Data representation of the pixel samples. Each sample shall have the same pixel representation. See Section C.8.12.1.1.3 for specialization of this Attribute.
Samples per Pixel (0028,0002) 1 Number of samples (planes) per image. See C.8.12.1.1.4 for specialization of this Attribute.
Planar Configuration (0028,0006) 1C Indicates whether the pixel data are sent color-by-plane or color-by-pixel. Required if Samples per Pixel (0028,0002) has a value greater than 1. See C.8.12.1.1.5 for specialization of this Attribute.
Content Time (0008,0033) 1C The time the image pixel data creation started. Required if the Image is part of a series in which the images are temporally related. Note: This Attribute was formerly known as Image Time.
Lossy Image Compression (0028,2110) 2 Specifies whether an Image has undergone lossy compression. Enumerated Values: 00 = Image has NOT been subjected to lossy compression. 01 = Image has been subjected to lossy compression. See C.7.6.1.1.5
Referenced Image Sequence (0008,1140) 1C A Sequence that references other images significantly related to this image. One or more items are permitted in this sequence. Required if Image Type (0008,0008) Value 3 is present and has a value of "STEREO L" or "STEREO R". May also be present otherwise. See Section C.8.12.1.1.7.
>Include ‘Image SOP Instance Reference Macro’ Table 10-3
>Purpose of Reference Code Sequence (0040,A170) 2 Describes the purpose for which the reference is made. Zero or one item shall be included in this sequence.
>>Include Code Sequence Macro Table 8.8-1 Defined Context ID 7201
Window Center (0028,1050) 3 Window Center for display. See C.11.2.1.2 for further explanation. Meaningful only if Photometric Interpretation (0028,0004) is MONOCHROME2.
Window Width (0028,1051) 1C Window Width for display. See C.11.2.1.2 for further explanation. Required if Window Center (0028,1050) is present.
Anatomic Region Sequence (0008,2218) 1C Sequence that identifies the anatomic region of interest in this image (i.e. external anatomy, surface anatomy, or general region of the body). Only a single Item shall be included in this sequence. Required if Number of Frames (0028,0008) is present and Specimen Description Sequence (0040,0560) is absent. May be present otherwise.
>Include ‘Code Sequence Macro’ Table 8.8-1 Defined CID 4040 is defined for the Video Endoscopic IOD. For other IODs, no Context ID is defined.
>Anatomic Region Modifier Sequence (0008,2220) 3 Sequence of Items that modifies the anatomic region of interest of this image One or more Items are permitted in this Sequence.
>>Include ‘Code Sequence Macro’ Table 8.8-1 Baseline CID 2.
Include ‘Primary Anatomic Structure Macro’ Table 10.4-8 No Context ID is defined. These Type 3 Attributes are not appropriate when Specimen Description Sequence (0040,0560) is present, as it includes the Primary Anatomic Structure Macro for each specimen in the image.
Channel Description Code Sequence (0022,001A) 3 Describes the light color used for each channel to generate the image. If Photometric Interpretation (0028,0004) has one of the YBR values, the meaning is for pixel data in an equivalent RGB encoding. Note: Interpretation and representation of RGB images rely on the assumption that the red channel really contains the red wavelength range of illumination light, the blue channel the blue wavelength range, etc. Some modalities use the RGB Photometric Interpretation as a container representing 3 channels of any illumination wavelength. Shall have the same number of items as the value of Samples per Pixel (0028,0002). The channels shall be described in the order in which the channels are encoded.
>Include ‘Code Sequence Macro’ Table 8.8-1 Baseline CID 4206.
Pixel Spacing (0028,0030) 3 Physical distance in the imaging target (patient or specimen) between the center of each pixel, specified as a numeric pair – adjacent row spacing \ adjacent column spacing, in mm. See 10.7.1.3.

C.8.12.1.1 VL Image Module Attribute Descriptions

C.8.12.1.1.1 Photometric Interpretation

The Enumerated Values of Photometric Interpretation (0028,0004) shall be:

MONOCHROME2

RGB

YBR_FULL_422

YBR_PARTIAL_420

YBR_RCT

YBR_ICT

Note: There is no formal color space defined, hence “false” color applications that encode near-visible light images may be encoded, for example, as RGB.

C.8.12.1.1.2 Bits Allocated, Bits Stored, and High Bit

The Enumerated Value of Bits Allocated (0028,0100) shall be 8; the Enumerated Value of Bits Stored (0028,0101) shall be 8; and the Enumerated Value of High Bit (0028,0102) shall be 7.

C.8.12.1.1.3 Pixel Representation

The Enumerated Value of Pixel Representation (0028,0103) shall be 0.

C.8.12.1.1.4 Samples per Pixel

The Enumerated Values of Samples per Pixel (0028,0002) shall be as follows: If the value of Photometric Interpretation (0028,0004) is MONOCHROME2, then the Enumerated Value of Samples per Pixel (0028,0002) shall be one (1). If the value of Photometric Interpretation (0028,0004) is RGB or YBR_FULL_422 or YBR_PARTIAL_420 or YBR_RCT or YBR_ICT, then the Enumerated Value of Samples per Pixel (0028,0002) shall be three (3).

C.8.12.1.1.5 Planar Configuration

If present, the Enumerated Value of Planar Configuration (0028,0006) shall be 0. This value shall be present if Samples per Pixel (0028,0002) has a value greater than 1.

C.8.12.1.1.6 Image Type

The Image Type attribute identifies important image characteristics in a multiple valued data element. For Visible Light, Image Type is specialized as follows:

a. Value 1 shall identify the Pixel Data Characteristics in accordance with Section C.7.6.1.1.2; Enumerated Values are: ORIGINAL and DERIVED;

b. Value 2 shall identify the Patient Examination Characteristics in accordance with Section C.7.6.1.1.2; Enumerated Values are: PRIMARY and SECONDARY.

c. Value 3 may be absent, but if present shall identify the members of a stereo pair, in which case Referenced Image Sequence (0008,1140) is used to identify the other member of the pair. If present, the Enumerated Values are:

STEREO L Image is the left image (relative to the observer's left) of a stereo pair acquisition;
STEREO R Image is the right image (relative to the observer's right) of a stereo pair acquisition.

d. Other Values are implementation specific (optional).

C.8.12.1.1.7 Referenced Image Sequence

When Image Type (0008,0008) Value 3 is STEREO L or STEREO R, Referenced Image Sequence (0008,1140) shall be used to identify the corresponding SOP Instance of the Stereoscopic acquisition. In this case, either:

C.8.12.2 Slide Coordinates Module

The table in this Section contains Attributes that describe Slide Coordinates. Slide Coordinates provide a means to locate an image within a given Frame of Reference.

Notes: 1. A Frame of Reference (identified by a Frame of Reference UID) typically only applies to a single mounting of a slide on a particular microscope stage; there is no guarantee that a subsequent mounting of the slide, even on the same equipment, will allow reproducible positioning to the exact same location. These attributes allow consistent location of multiple images within the Series of a single Frame of Reference.

2. There is no a priori correspondence of pixels to Slide Coordinates. Therefore, the geometrical symmetry point through the pixel plane of the digital microscope may not correspond to the center of a pixel. The geometrical symmetry point could be between pixels.

3. This module formerly included a Type 3 attribute Pixel Spacing Sequence (0040,08D8), and subsidiary attributes; see PS 3.3-2009. Pixel spacing is an attribute of the image acquisition, not the slide coordinates, and is inappropriate for this Module. It is now conveyed by Pixel Spacing (0028,0030) in the VL Image Module or the Pixel Measures Functional Group.

Table C.8-78Slide Coordinates Module Attributes

Attribute Name Tag Type Attribute Description
Image Center Point Coordinates Sequence (0040,071A) 2 The coordinates of the center point of the Image in the Slide Coordinate System Frame of Reference. Zero or one item shall be included in this sequence. See 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. See Figure C.8-16.
>Y Offset in Slide Coordinate System (0040,073A) 1 The Y offset in millimeters from the Origin of the Slide Coordinate System. See Figure C.8-16.
>Z Offset in Slide Coordinate System (0040,074A) 2 The Z offset in microns from the image substrate reference plane (i.e. utilized surface of a glass slide).

C.8.12.2.1 Slide Coordinates Attribute Descriptions

C.8.12.2.1.1 Image Center Point Coordinates Sequence

This Section defines the Slide Coordinate System and specifies the Attributes that shall be used to describe the location of the center point of the Image pixel plane (as captured through a microscope) in the Slide Coordinate System Frame of Reference.

Note: In Slide Microscopy (SM), the Microscope is equipped with a moveable Stage and position sensors that enable storage of the location of the center point of the displayed image with respect to the examined Specimen.

The Stage is the part of the Microscope to which the Slide is attached for viewing. The Objective Lens is the lens that is closest to the Specimen. The Top Surface of the Slide is the surface of the Slide on which the Specimen is mounted. The Bottom Surface of the Slide is the opposite surface. This Specification presumes that: 1) the Slide is rectangular; 2) the Top Surface of the Slide is oriented toward the Objective Lens of the Microscope; and 3) the Bottom Surface of the Slide is in perfect contact with the Microscope Stage when the Slide is attached to the Stage for viewing.

Notes: 1. The Label of the Slide is presumed to be mounted-on or written-on the Top Surface of the Slide.

2. Specification of the mechanical form, function, or tolerances of the Microscope are outside the scope of this Standard.

Figure C.8-16 depicts the Top Surface of the Slide on the Microscope Stage from the perspective of the Objective Lens. This is Reference Slide Orientation. The X, Y, and Z axes of the Slide Coordinate System in Reference Slide Orientation are defined as follows. The Y-axis is a line that nominally represents the Left Edge of the Slide. The X-axis is a line that is orthogonal to the Y-axis and nominally represents the Specimen Edge of the Slide. The Z-axis is a line that passes through the intersection of the X-axis and Y-axis and is orthogonal to the Microscope Stage. The Origin (0,0,0) of the Slide Coordinate System is the point of intersection of the X, Y, and Z axes.

[pic]

Figure C.8-16 REFERENCE SLIDE ORIENTATION

Notes: 1. An improperly-placed coverslip or Specimen that overlaps an Edge of a Slide is not considered part of the Edge a Slide for purposes of defining the Slide Coordinate System. However, such objects may cause inaccurate positioning of the Slide on the Stage.

2. If the Left Edge and Specimen Edge of the Slide are not orthogonal (e.g. the Slide is damaged or defective or the Specimen Edge is curvilinear), then the lower left-hand corner of the Slide may not be located at the Origin.

3. The definitions of X, Y, and Z axes are the same for inverted microscopes, with the Top Surface of the slide (i.e. Specimen side of the Slide) still being closest to the Objective Lens.

4. The origin of a Frame of Reference is arbitrary (see C.7.4.1), but its nominal location for consistency of slide coordinates is defined in this section.

Figure C.8-17 depicts the Z-axis center point location. The X-axis value of Image Center Point Location (0040,073A) shall increase from the Origin toward the Right Edge in Reference Slide Orientation. The Y-axis value of Image Center Point Location (0040,073A) shall increase from the Origin toward the Label Edge in Reference Slide Orientation. The Z-axis value of Image Center Point Location (0040,073A) shall be nominally referenced as zero at the image substrate reference plane (i.e. the top surface of a glass slide) and shall increase in a positive fashion coincident with increased distance from the substrate surface.

[pic]Figure C.8-17 Z-AXIS CENTER POINT LOCATION, VIEW FROM RIGHT EDGE OF SLIDE

C.8.12.3 VL Whole Slide Microscopy Series Module

Table C.8.12.3-1 specifies attributes for the VL Whole Slide Microscopy Series Module, including specialization of attributes in the General Series Module for use in the VL Whole Slide Microscopy Series Module.

Table C.8.12.3-1VL WHOLE SLIDE MICROSCOPY SERIES MODULE ATTRIBUTES

Attribute Name Tag Type Attribute Description
Modality (0008,0060) 1 Type of equipment that originally acquired the data used to create the images in this Series. Enumerated Values: SM See section C.7.3.1.1.1 for further explanation.
Referenced Performed Procedure Step Sequence (0008,1111) 1C Uniquely identifies the Performed Procedure Step SOP Instance to which the Series is related (e.g. a Modality or General-Purpose Performed Procedure Step SOP Instance). Only a single Item shall be included in this sequence. Required if the Modality Performed Procedure Step SOP Class or General Purpose Performed Procedure Step SOP Class is supported.
>Include ‘SOP Instance Reference Macro' Table 10-11

C.8.12.4 VL Whole Slide Microscopy Image Module

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

Table C.8.12.4-1VL WHOLE SLIDE MICROSCOPY IMAGE MODULE ATTRIBUTES

Attribute Name Tag Type Attribute Description
Image Type (0008,0008) 1 Image identification characteristics. See 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 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 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 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 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 C.8.12.4.1.3
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 C.8.12.4.1.4 and 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 C.8.12.4.1.4
Samples Per Pixel (0028,0002) 1 Number of samples (color planes) per frame in this image. Enumerated values: 1 or 3. See 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 sent color-by-plane or color-by-pixel. Required if Samples per Pixel (0028,0002) has a value greater than 1. Enumerated Value: 0 = color-by-pixel
Number of Frames (0028,0008) 1 Number of frames in a multi-frame image. If Image Type (0008,0008) Value 3 is LOCALIZER or LABEL, Enumerated Value is 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. Enumerated Values: 8, 16
High Bit (0028,0102) 1 Most significant bit for pixel sample data. Enumerated Values: 7, 15
Pixel Representation (0028,0103) 1 Data representation of pixel samples. Enumerated Value: 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) 1 Duration of the image acquisition in ms.
Lossy Image Compression (0028,2110) 1 Specifies whether an Image has undergone lossy compression. Enumerated Values: 00 - Image has NOT been subjected to lossy compression. 01 - Image has been subjected to lossy compression. See C.7.6.1.1.5
Lossy Image Compression Ratio (0028,2112) 1C See C.7.6.1.1.5 for further explanation. Required if Lossy Image Compression (0028,2110) equals 01.
Lossy Image Compression Method (0028,2114) 1C A label for the lossy compression method(s) that have been applied to this image. See C.7.6.1.1.5 for further explanation. May be multi valued if successive lossy compression steps have been applied; the value order shall correspond to the values of Lossy Image Compression Ratio (0028,2112). Required if Lossy Image Compression (0028,2110) equals 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. Enumerated value 0 Required if Photometric Interpretation (0028,0004) is MONOCHROME2.
Rescale Slope (0028,1053) 1C m in the equation specified by Rescale Intercept (0028,1052). Enumerated value 1 Required if Photometric Interpretation (0028,0004) is MONOCHROME2.
Volumetric Properties (0008,9206) 1 Indication if geometric manipulations are possible with frames in the SOP Instance. See C.8.16.2.1.2. Enumerated Value: 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 acquisition focal planes used for extended depth of field. Required if Extended Depth of Field (0048,0012) value is YES
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
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 C.10.7.1.1.

C.8.12.4.1 VL 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.8.12.4-2VL WHOLE SLIDE MICROSCOPY IMAGE FLAVORS

LOCALIZER Collected for the purpose of planning or navigating other images.
VOLUME Set of frames that define a regularly sampled volume
LABEL Purpose of image is to capture the slide label; any non-label area captured is incidental to that purpose.

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

Table C.8.12.4-3VL WHOLE SLIDE MICROSCOPY 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.

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 the Slice Thickness (0018,0050) attribute of the Pixel Measures Functional Group (see C.7.6.16.2.1.1).

C.8.12.4.1.3 Total Pixel Matrix Columns, Rows

Total Pixel Matrix Columns (0048,0006) and Total Pixel Matrix Rows (0048,0007) 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 the Pixel Spacing (0028,0030) attribute of the Pixel Measures Functional Group (see C.7.6.16.2.1.1).

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 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, the Image Orientation (Slide) attribute 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

Photometric Interpretation (0028,0004) shall be one of these Enumerated Values (see C.7.6.3.1.2):

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 involve color space transformations, YBR_ICT for irreversible JPEG 2000 transfer syntaxes, YBR_RCT for reversible JPEG 2000 transfer syntaxes, and YBR_FULL_422 for other lossy compressed transfer syntaxes.

Note: 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.

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.

Samples per Pixel (0028,0002) shall be 1 for MONOCHROME2, and 3 otherwise.

C.8.12.5 Optical Path Module

Table C.8.12.5-1 specifies the attributes of the optical paths used in the VL imaging. Each optical path is a combination of illumination, filters, lenses, and sensors, and each combination is identified for possible reference by attributes in other modules. Additional optical path parameters may be specified in the Acquisition Context Module.

Table C.8.12.5-1OPTICAL PATH MODULE ATTRIBUTES

Attribute Name Tag Type Attribute Description
Optical Path Sequence (0048,0105) 1 Describes the optical paths used during the acquisition of this image. One or more Items shall be included in this sequence. See C.8.12.5.1.1
>Optical Path Identifier (0048,0106) 1 Identifier for the optical path specified in the Sequence Item. The identifier shall be unique for each Item within the Optical Path Sequence.
>Optical Path Description (0048,0107) 3 Description of the optical path specified in the Sequence Item.
>Illuminator Type Code Sequence (0048,0100) 3 Type of illuminator. Only a single Item is permitted in this sequence.
>>Include ‘Code Sequence Macro’ Table 8.8.1 Context ID may be defined in the IOD constraints.
>Illumination Wave Length (0022,0055) 1C Nominal wavelength of the illuminator in nm. Required if Illumination Color Code Sequence (0048,ee08) is not present. May be present otherwise.
>Illumination Color Code Sequence (0048,0108) 1C Color of the illuminator. Only a single Item shall be included in this sequence. Required if Illumination Wave Length (0022,0055) is not present. May be present otherwise.
>>Include ‘Code Sequence Macro’ Table 8.8.1 Context ID may be defined in the IOD constraints.
>Illumination Type Code Sequence (0022,0016) 1 Coded value for illumination method. See C.8.12.5.1.2. One or more Items shall be included in this sequence.
>>Include ‘Code Sequence Macro’ Table 8.8.1 Context ID may be defined in the IOD constraints.
>Light Path Filter Type Stack Code Sequence (0022,0017) 3 Filters used in the light source (excitation) path. One or more Items are permitted in this sequence. See C.8.12.5.1.3.
>>Include ‘Code Sequence Macro’ Table 8.8.1 Context ID may be defined in the IOD constraints.
>Light Path Filter Pass-Through Wavelength (0022,0001) 3 Nominal pass-through wavelength of light path filter(s) in nm
>Light Path Filter Pass Band (0022,0002) 3 Pass band of light path filter(s) in nm. This Attribute has two Values. The first is the shorter and the second the longer wavelength relative to the peak. The values are for the – 3dB nominal (1/2 of peak) pass through intensity. One of the two Values may be zero length, in which case it is a cutoff filter.
>Image Path Filter Type Stack Code Sequence (0022,0018) 3 Describes stack of filters used in image (emission) path between the imaging target and the optical sensor. One or more items are permitted in this sequence. See C.8.12.5.1.3.
>>Include ‘Code Sequence Macro’ Table 8.8.1 Context ID may be defined in the IOD constraints.
>Image Path Filter Pass-Through Wavelength (0022,0003) 3 Nominal pass-through wavelength of image path filter(s) in nm
>Image Path Filter Pass Band (0022,0004) 3 Pass band of image path filter(s) in nm. This Attribute has two Values. The first is the shorter and the second the longer wavelength relative to the peak. The values are for the – 3dB nominal (1/2 of peak) pass through intensity. One of the two Values may be zero length, in which case it is a cutoff filter
>Lenses Code Sequence (0022,0019) 3 Lenses that were used in this optical path. One or more items are permitted in this sequence.
>>Include ‘Code Sequence Macro’ Table 8.8-1 Context ID may be defined in the IOD constraints.
>Condenser Lens Power (0048,0111) 3 Nominal power of the condenser lens
>Objective Lens Power (0048,0112) 3 Nominal power of the objective lens. If a single lens is used as both condenser and objective, its power is specified in this attribute.
>Objective Lens Numerical Aperture (0048,0113) 3 Nominal numerical aperture of the objective lens.
>Channel Description Code Sequence (0022,001A) 1C Describes the light color sensed for each channel to generate the image. Required if this differs from the natural interpretation. Notes: 1. For MONOCHROME2, the natural interpretation is the full visible light spectrum. A full spectrum sensor may be presented with light of only a single color based on illumination and filters. 2. Equipment may use a color Photometric Interpretation (RGB, YBR) as a container representing up to 3 channels of any detected wavelength. Shall have the same number of Items as the value of Samples per Pixel Used (0028,0003) if present, or otherwise the value of Samples per Pixel (0028,0002). The channels shall be described in the order in which the channels are encoded.
>>Include ‘Code Sequence Macro’ Table 8.8.1 Context ID may be defined in the IOD constraints.
>Palette Color Lookup Table Sequence (0048,0120) 3 For MONOCHROME2 images, provides a transform of the pixel values with this optical path into an RGB color representation. The LUT provides a mapping to an appropriate color or pseudo-color for display purposes. Only a single Item is permitted in this sequence.
>>Include ‘Palette Color Lookup Macro’ Table C.7-22a
>ICC Profile (0028,2000) 1C An ICC Profile encoding the transformation of device-dependent stored pixel values into PCS-Values. See C.8.12.5.1.4 Required if Photometric Interpretation (0028,0004) is not MONOCHROME2, or if Palette Color Lookup Table Sequence (0048,0120) is present.

C.8.12.5.1 Optical Path Attribute Descriptions

C.8.12.5.1.1 Optical Path Sequence and Optical Path Identifier

The Optical Path Sequence (0048,0105) shall include an Item for every optical path used in the acquisition of the current image.

For single frame images that do not include the Multi-frame Functional Groups Module, this Sequence shall include only one Item.

For images that use the Multi-frame Functional Groups Module, the optical path associated with each frame is identified by reference to the Optical Path Identifier (0048,0106) of this Sequence (see Optical Path Identification Sequence (0048,0207) in Section C.8.12.6.2). The Optical Path Sequence may include Items for defined optical paths that are not referenced by any frame.

For Whole Slide Microscopy Image LOCALIZER images (see C.8.12.4.1.1 and C.8.12.7), all the optical paths associated with referenced images shall be described in Items of this Optical Path Sequence. The optical path associated with each referenced frame is identified in the Referenced Image Navigation Sequence (0048,0200) by reference to an Optical Path Identifier (0048,0106) of this Sequence. The Optical Path Identifiers used in the LOCALIZER image do not have to be identical to those used in the referenced images.

Notes: 1. For example, each of four referenced images may use a different optical path (color), and within each of those image SOP Instances the single Optical Path Sequence Item is identified as “1”, although the meaning of optical path “1” is different for each image. The LOCALIZER, however, must include all four optical paths with distinct identifiers “1”, “2”, “3”, and “4”.

2. The Optical Path Identifier is not necessarily numeric; it is a string of up to 16 characters (VR SH).

C.8.12.5.1.2 Illumination Type Code Sequence

Illumination Type Code Sequence (0022,0016) specifies the type of illumination of the imaging target. This attribute may include multiple Items, as some techniques may involve multiple methods, or some method identifiers may not be completely descriptive.

Note: For example, this attribute might include two items, (111741, DCM, “Transmission illumination”) and (111748, DCM, “Differential interference contrast”) to indicate “Transmission DIC”.

The type of illumination often prescribes the set of optical path components such as filters and prisms, and their arrangement in the optical path.

Note: For instance, phase contrast illumination will utilize a condenser annulus and a phase contrast plate; this may be indicated by an item (111747, DCM, “Phase contrast illumination”) in this attribute, but with no further specification in the filters and lenses identification attributes.

C.8.12.5.1.3 Light Path and Image Path Filter Type Stack Code Sequences

In some optical imaging methods, e.g., epifluorescence, there may be a single light path with its associated imaging components that is used in both illumination/excitation of the imaging target and in the transmitted/emitted path to the imaging sensor. In this case, the optical components are to be specified in the Image Path Filter Type Stack Code Sequence (0022,0018).

C.8.12.5.1.4 ICC Profile

ICC Profile (0028,2000) provides the transform for mapping stored color pixel values into ICC standard color Profile Connection Space (PCS). For MONOCHROME2 pixels that have a preferred color rendering through the Palette Color Lookup Table Sequence (0048,0120), this attribute provides a mapping of that preferred RGB color rendering into PCS. The ICC Profile shall follow the requirements specified in Section C.11.15.1.1.

C.8.12.6 Whole Slide Microscopy Functional Group Macros

The following sections contain Functional Group macros specific to the VL Whole Slide Microscopy Image IOD.

Note: The attribute descriptions in the Functional Group Macros are written as if they were applicable to a single frame (i.e., the macro is part of the Per-frame Functional Groups Sequence). If an attribute is applicable to all frames (i.e. the macro is part of the Shared Functional Groups Sequence) the phrase “this frame” in the attribute description shall be interpreted to mean “for all frames”.

C.8.12.6.1 Plane Position (Slide) Macro

Table C.8.12.6.1-1 specifies the attributes of the Plane Position (Slide) Functional Group macro.

Table C.8.12.6.1-1PLANE POSITION (SLIDE) MACRO ATTRIBUTES

Attribute Name Tag Type Attribute Description
Plane Position (Slide) Sequence (0048,021A) 1 Describes position of frame in the Total Pixel Matrix and in the Slide Coordinate System Frame of Reference. Only a single Item shall be included in this Sequence.
>Column Position In Total Pixel Matrix (0048,021E) 1 The column position of the top left hand pixel of the frame in the Total Pixel Matrix (see C.8.12.4.1.1). The column position of the top left pixel of the Total Pixel Matrix is 1.
>Row Position In Total Pixel Matrix (0048,021F) 1 The row position of the top left hand pixel of the frame in the Total Pixel Matrix (see C.8.12.4.1.1). The row position of the top left pixel of the Total Pixel Matrix is 1.
>X Offset in Slide Coordinate System (0040,072A) 1 The X offset in mm from the Origin of the Slide Coordinate System. See Figure C.8-16.
>Y Offset in Slide Coordinate System (0040,073A) 1 The Y offset in mm from the Origin of the Slide Coordinate System. See Figure C.8-16.
>Z Offset in Slide Coordinate System (0040,074A) 1 The Z offset in μm from the Origin of the Slide Coordinate System, nominally the surface of the glass slide substrate. See Figure C.8-17 Note: Required even if only a single focal plane was acquired.

C.8.12.6.2 Optical Path Identification Macro

Table C.8.12.6.2-1 specifies the attributes of the Optical Path Identification Functional Group macro.

Table C.8.12.6.2-1OPTICAL PATH IDENTIFICATION MACRO ATTRIBUTES

Attribute Name Tag Type Attribute Description
Optical Path Identification Sequence (0048,0207) 1 Identifies the optical path characteristics of this frame. Only a single Item shall be included in this sequence.
>Optical Path Identifier (0048,0106) 1 Uniquely identifies the path described in the Optical Path Sequence (0048,0105) by reference to an Item with the same Optical Path Identifier (0048,0106) value. See C.8.12.5.

C.8.12.6.3 Specimen Reference Macro

Table C.8.12.6.3-1 specifies the attributes of the Specimen Reference Functional Group macro. This allows association of the frame with specific specimens imaged on the same slide (e.g., tissue micro-arrays).

Table C.8.12.6.3-1SPECIMEN REFERENCE MACRO ATTRIBUTES

Attribute Name Tag Type Attribute Description
Specimen Reference Sequence (0048,0110) 2 Identifies specimens that may be visible in this frame, and which are fully identified in the Specimen Description Sequence (0040,0560). Zero or more Items shall be included in this sequence.
>Specimen UID (0040,0554) 1 Unique Identifier for Specimen. See Section C.7.6.22.1.2.

C.8.12.7 Multi-Resolution Navigation Module

Table C.8.12.7-1 specifies the Attributes that describe the Multi-Resolution Navigation Module, used in Whole Slide Microscopy LOCALIZER images.

Table C.8.12.7-1MULTI-RESOLUTION NAVIGATION MODULE ATTRIBUTES

Attribute Name Tag Type Attribute Description
Referenced Image Navigation Sequence (0048,0200) 1 Identification of correspondence between areas of the Pixel Data (07FE,0010) and frames of higher resolution images. One or more Items shall be included in this sequence.
>Include ‘SOP Instance Reference Macro’ Table 10-11 Referenced Image Instance
>Referenced Frame Number (0008,1160) 1 Referenced Frame Number within Referenced Image.
>Top Left Hand Corner of Localizer Area (0048,0201) 1 Top Left Hand Corner of Localizer image pixel area corresponding to referenced frame, specified as column\row. Column is the horizontal offset and row is the vertical offset.
>Bottom Right Hand Corner of Localizer Area (0048,0202) 1 Bottom Right Hand Corner of Localizer image pixel area corresponding to referenced frame, specified as column\row. Column is the horizontal offset and row is the vertical offset.
>Pixel Spacing (0028,0030) 1 Pixel Spacing in Referenced Image, specified as a numeric pair – adjacent row spacing \ adjacent column spacing, in mm.
>Z Offset in Slide Coordinate System (0040,074A) 1 The Z offset of the referenced frame from the Slide Coordinates System reference plane, in microns
>Samples per Pixel (0028,0002) 1 The number of samples (color planes) containing information in the referenced image.
>Optical Path Identifier (0048,0106) 1 Identifies the optical path used in acquiring the referenced Frame by reference to an Item in the Optical Path Sequence (0048,0105) of the current SOP Instance. See C.8.12.5.

C.8.12.8 Slide Label Module

Table C.8.12.8-1 specifies the Attributes that describe the interpretation of a scanned Slide Label.

Table C.8.12.8-1SLIDE LABEL MODULE ATTRIBUTES

Attribute Name Tag Type Attribute Description
Barcode Value (2200,0005) 2 Barcode interpreted from the scanned slide label. Note: This may be the same as the Container Identifier (0040,0512).
Label Text (2200,0002) 2 Label text interpreted from the scanned slide label, e.g., by optical character recognition.