Z- Planes
A.32. X.4.1.2 Plane Position (Slide)
C.8.12. X5 Multi-Resolution Navigation Module
Table C.8.12.X5-1 specifies the Attributes that describe the Multi-Resolution Navigation Module, used in Whole Slide Microscopy LOCALIZER images.
Table C.8.12.X5-1
MULTI-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 present.
>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.x3.
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.
Update PS 3.3 C.8.12.1
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.
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Table C.8-77
VL IMAGE MODULE ATTRIBUTES
Attribute Name Tag Type Attribute Description
…
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.
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Update PS 3.3 C.8.12.2
C.8.12.2 Slide Coordinates Module
The table in this Section contains Attributes that describe Slide Coordinates. Slide Coordinates provide a means to position a robotic Microscope Stage reproduceably with respect to the pixel plane of
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the digital Microscope 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 900
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 905
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.8-78
Slide Coordinates Module Attributes
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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 present in the 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
adjacent pixels along the axis specified by Coordinate System Axis Code Sequence (0040,08DA).
>Measurement Units Code Sequence
(0040,08EA) 1 Units of the measurement. This sequence shall contain exactly one item.
>>Include ‘Code Sequence Macro’ Table 8.8-1 Baseline Context ID is 82.
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.
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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 in is Mmounted. 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.
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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 includes nominally represents the Left Edge of the Slide. The X-axis is a line that is orthogonal to the Y-axis and
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nominally represents includes at least one point of the Specimen Edge of the Slide. The Z-axis is a line that passes through the intersection of the X-Z-axis and Y-Z-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.
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.
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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.
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Origin
Label
Y Increase
X Increase
Specimen Edge Label Edge
Right-Edge Left Edge
Specimen
Glass Slide
Microscope Stage
Figure C.8-16
REFERENCE SLIDE ORIENTATION
Origin
Z Increase
Glass SlideSubstrate Specimen
Cover Slip
MICROSCOPE
Y Increase
Figure C.8-17
Z-AXIS CENTER POINT LOCATION, VIEW FROM RIGHT EDGE OF SLIDE
Add new attribute and defined terms to C.10.4 and C.10.5
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C.10.4 Displayed Area Module
This Module describes Attributes required to define a Specified Displayed Area space.
The Specified Displayed Area is that portion of the image displayed on the device.
…
Table C.10-4
DISPLAYED AREA MODULE ATTRIBUTES
Attribute Name Tag Type Attribute Description
Displayed Area Selection Sequence
(0070,005A) 1 A sequence of Items each of which describes the displayed area selection for a group of images or frames. Sufficient Items shall be present to describe every image and frame listed in the Presentation State Relationship Module.
One or more Items shall be present.
>Referenced Image Sequence (0008,1140) 1C Sequence of Items where each Item provides reference to a selected set of Image SOP Class/SOP Instance pairs that are defined in the Presentation State Relationship Module.
One or more Items shall be present.
Required if the displayed area selection in this Item does not apply to all the images and frames listed in the Presentation State Relationship Module.
>>Include ‘Image SOP Instance Reference Macro’ Table 10-3
>Pixel Origin Interpretation (0048,0301) 1C For a referenced multi-frame image, specifies whether the Displayed Area Top Left Hand Corner (0070,0052) and
Displayed Area Bottom Right Hand Corner (0070,0053) are to be interpreted relative to the individual frame pixel origins, or relative to the Total Pixel Matrix origin (see C.8.12.X2.1.4).
Required if the value of Referenced SOP Class UID (0008,1150) within Referenced Image Sequence (0008,1140) is
1.2.840.10008.5.1.4.1.1.77.1.6 (VL Whole Slide Microscopy Image). May be present otherwise.
Enumerated Values:
FRAME – relative to individual frame VOLUME – relative to Total Image Matrix If not present, TLHC and BRHC are defined relative to the frame pixel origins.
>Displayed Area Top Left Hand Corner
(0070,0052) 1 The top left (after spatial transformation) pixel in the referenced image to be displayed, given as column\row. Column is the horizontal (before spatial transformation) offset (X) and row is the vertical (before spatial
transformation) offset (Y) relative to the origin of the pixel data before spatial transformation, which is 1\1. See Figure C.10.4-1.
Notes: 1. In scale to fit mode, the Displayed Area Top Left Hand Corner (TLHC)and Bottom Right Hand Corner (BRHC) have the effect of defining how any zoom or magnification and/or pan has been applied to select a region of an image to be displayed (the Specified Displayed Area), without assuming anything about the size of the actual display.
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2. The TLHC and BRHC may be outside the boundaries of the image pixel data (e.g. the TLHC may be 0 or negative, or the BRHC may be greater than Rows or Columns), allowing minification or placement of the image pixel data within a larger Specified Displayed Area. There is no provision to position a zoomed selected sub-area of the image pixel data within a larger Specified Displayed Area.
3. When Pixel Origin Interpretation (0048,0301) value is VOLUME, the selected Display Area may extend across multiple frames, and may include pixel locations for which there is no pixel data (outside the edge of the imaged volume, not encoded in a sparse encoding, or not within explicitly selected frames).
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C.10.5 Graphic Annotation Module
This Module defines Attributes of vector graphics and text annotation that shall be made available by a display device to be applied to an image. The graphics and text are defined in position and size relative to the image pixel coordinates or the Specified Displayed Area space (defined in C.10.4 Displayed Area Module). A Graphic Annotation shall be related to an Image.
Note: This Module uses a Sequence of Items rather than a Repeating Group to avoid limiting the maximum number of annotation items that may be present. The use of a Repeating Group would limit the number of items to 16. The use of Repeating Groups is also noted in PS 3.5 to be deprecated.
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Table C.10-5
GRAPHIC ANNOTATION MODULE ATTRIBUTES
Attribute Name Tag Type Attribute Description
Graphic Annotation Sequence (0070,0001) 1 A sequence of Items each of which
represents a group of annotations composed of graphics or text or both.
One or more Items shall be present.
>Referenced Image Sequence (0008,1140) 1C Sequence of Items where each Item provides reference to a selected set of Image SOP Class/SOP Instance pairs that are defined in the Presentation State Relationship Module. One or more Items shall be present.
Required if graphic annotations in this Item do not apply to all the images and frames listed in the Presentation State Relationship Module.
>>Include ‘Image SOP Instance Reference Macro’ Table 10-3
>Graphic Layer (0070,0002) 1 The layer defined in the Graphic Layer Module C.10.7 in which the graphics or text is to be rendered.
>Text Object Sequence (0070,0008) 1C Sequence that describes a text annotation.
One or more Items may be present.
Either one or both of Text Object Sequence (0070,0008) or Graphic Object Sequence (0070,0009) are required .
>>Bounding Box Annotation Units
(0070,0003) 1C Units of measure for the axes of the text bounding box.
Defines whether or not the annotation is Image or Displayed Area relative. Both dimensions shall have the same units.
Enumerated Values:
PIXEL = Image relative position specified with sub-pixel resolution such that the origin, which is at the Top Left Hand Corner (TLHC) of the TLHC pixel, is 0.0\0.0, the Bottom Right Hand Corner (BRHC) of the TLHC pixel is 1.0\1.0, and the BRHC of the BRHC pixel is Columns\Rows (see figure C.10.5-1).
The values must be within the range 0\0 to Columns\Rows.
DISPLAY = Fraction of Specified Displayed Area where 0.0\0.0 is the TLHC and 1.0\1.0 is the BRHC. The values must be within the range 0.0 to 1.0.
MATRIX = Image relative position specified with sub-pixel resolution such that the origin, which is at the Top Left Hand Corner (TLHC) of the TLHC pixel of the Total Pixel Matrix, is 0.0\0.0, the Bottom Right Hand Corner (BRHC) of the TLHC pixel is 1.0\1.0, and the BRHC of the BRHC pixel of the Total Pixel Matrix is Total Pixel Matrix Columns\Total Pixel Matrix Rows (see C.8.12.X2.1.3). The values must be within the range 0.0\0.0 to Total Pixel Matrix
Columns\Total Pixel Matrix Rows.
MATRIX may be used only if the value of Referenced SOP Class UID (0008,1150) within Referenced Image Sequence (0008,1140) is
1.2.840.10008.5.1.4.1.1.77.1.6 (VL Whole Slide Microscopy Image).
Required if Bounding Box Top Left Hand Corner (0070,0010) or Bounding Box Bottom Right Hand Corner (0070,0011) is present.
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Changes to NEMA Standards Publication PS 3.4-2009
Digital Imaging and Communications in Medicine (DICOM)
Part 4: Service Class Specifications
In PS 3.4 Annex I add new SOP Class:
I.4 MEDIA STANDARD STORAGE SOP CLASSES Table I.4-1
Media Storage Standard SOP Classes
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SOP Class Name SOP Class UID IOD (See PS 3.3)
VL Whole Slide Microscopy Image Storage
1.2.840.10008.5.1.4.1.1.77.1.6 VL Whole Slide Microscopy Image
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Changes to NEMA Standards Publication PS 3.6-2009
Digital Imaging and Communications in Medicine (DICOM)
Part 6: Data Dictionary
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In PS 3.6 Section 6 add new data elements:
Tag Name Keyword VR VM
(0048,0001) Imaged Volume Width ImagedVolumeWidth FL 1 (0048,0002) Imaged Volume Height ImagedVolumeHeight FL 1 (0048,0003) Imaged Volume Depth ImagedVolumeDepth FL 1 (0048,0006) Total Pixel Matrix Columns TotalPixelMatrixColumns UL 1 (0048,0007) Total Pixel Matrix Rows TotalPixelMatrixRows UL 1 (0048,0008) Total Pixel Matrix Origin
Sequence
TotalPixelMatrixOriginSequen ce
SQ 1 (0048,0010) Specimen Label in Image SpecimenLabelInImage CS 1
(0048,0011) Focus Method FocusMethod CS 1
(0048,0012) Extended Depth of Field ExtendedDepthOfField CS 1 (0048,0013) Number of Focal Planes NumberOfFocalPlanes US 1
(0048,0014) Distance Between Focal Planes DistanceBetweenFocalPlanes FL 1 (0048,0015) Recommended Absent Pixel
CIELab Value
RecommendedAbsentPixelCI ELabValue
US 3 (0048,0100) Illuminator Type Code Sequence IlluminatorTypeCodeSequenc
e
SQ 1 (0048,0102) Image Orientation (Slide) ImageOrientationSlide DS 6 (0048,0105) Optical Path Sequence OpticalPathSequence SQ 1
(0048,0106) Optical Path Identifier OpticalPathIdentifier SH 1
(0048,0107) Optical Path Description OpticalPathDescription ST 1 (0048,0108) Illumination Color Code
Sequence
IlluminationColorCodeSequen ce
SQ 1 (0048,0110) Specimen Reference Sequence SpecimenReferenceSequence SQ 1 (0048,0111) Condenser Lens Power CondenserLensPower DS 1
(0048,0112) Objective Lens Power ObjectiveLensPower DS 1
(0048,0113) Objective Lens Numerical Aperture
ObjectiveLensNumericalApert ure
DS 1 (0048,0120) Palette Color Lookup Table
Sequence
PaletteColorLookupTableSequ ence
SQ 1 (0048,0200) Referenced Image Navigation
Sequence
ReferencedImageNavigationS equence
SQ 1 (0048,0201) Top Left Hand Corner of
Localizer Area
TopLeftHandCornerOfLocalize rArea
US 2
(0048,0202) Bottom Right Hand Corner of Localizer Area
BottomRightHandCornerOfLoc alizerArea
US 2 (0048,0207) Optical Path Identification
Sequence
OpticalPathIdentificationSeque nce
SQ 1 (0048,021A) Plane Position (Slide) Sequence PlanePositionSlideSequence SQ 1 (0048,021E) Column Position In Total Image
Pixel Matrix
ColumnPositionInTotalImageP ixelMatrix
SL 1 (0048,021F) Row Position In Total Image
Pixel Matrix
RowPositionInTotalImagePixel Matrix
SL 1 (0048,0301) Pixel Origin Interpretation PixelOriginInterpretation CS 1
1.2.840.10008.5.1.4.1.1.77.1.6 VL Whole Slide Microscopy Image Storage
SOP Class 3.4
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Add new rows to PS 3.6 Annex A Table A-3
Table A-3
CONTEXT GROUP UID VALUES
Context UID Context
Identifier
Context Group Name
...
1.2.840.10008.6.1.897 8120 WSI Referenced Image Purposes of Reference
1.2.840.10008.6.1.898 8121 WSI Microscopy Lens Type
1.2.840.10008.6.1.899 8122 Microscopy Illuminator and Sensor Color 1.2.840.10008.6.1.900 8123 Microscopy Illumination Method
1.2.840.10008.6.1.901 8124 Microscopy Filter
1.2.840.10008.6.1.902 8125 Microscopy Illuminator Type
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Changes to NEMA Standards Publication PS 3.16-2009
Digital Imaging and Communications in Medicine (DICOM)
Part 16: Content Mapping Resource
Coding Scheme
DCM 121311 Localizer
DCM 121350 Same acquisition at lower resolution DCM 121351 Same acquisition at higher resolution DCM 121352 Same acquisition at different focal depth DCM 121353 Same acquisition at different spectral band
DCM 121354 Imaged container label
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CID 8121 MICROSCOPY LENS TYPE
Context ID 8121 SRT A-0011A High power non-immersion lens
SRT A-0011B Oil immersion lens
SRT A-00118 Slide overview lens
CID 8122 MICROSCOPY ILLUMINATOR AND SENSOR COLOR Context ID 8122
Microscopy Illuminator and Sensor Color
1080
SRT R-102C0 Full Spectrum
SRT R-102BE Infrared
SRT G-A11A Red
SRT G-A11E Green
SRT G-A12F Blue
SRT R-102BF Ultraviolet
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CID 8123 MICROSCOPY ILLUMINATION METHOD Context ID 8123
DCM 111741 Transmission illumination
DCM 111742 Reflection illumination
DCM 111743 Epifluorescence illumination
DCM 111744 Brightfield illumination
DCM 111745 Darkfield illumination
DCM 111746 Oblique illumination
DCM 111747 Phase contrast illumination
DCM 111748 Differential interference contrast DCM 111749 Total internal reflection fluorescence
CID 8124 MICROSCOPY FILTER
Context ID 8124 SRT A-010E2 Green optical filter
SRT A-010DF Red optical filter SRT A-010DA Blue optical filter SRT A-010DC Infrared optical filter SRT A-010E1 Polarizing optical filter
SRT A-010DE Violet optical filter
SRT A-010DD Ultraviolet optical filter
SRT A-0010F Dichroic beamsplitter
SRT A-00121 Hoffman modulator
SRT A-0011D Darkfield stop
SRT A-0011C Rheinberg filter
SRT A-0011E Phase contrast plate
SRT A-00120 Condenser annulus
SRT A-0011F Nomarski prism
SRT A-00123 de Sénarmont compensator
DCM 111609 No filter
SRT A-00124 Xenon arc lamp SRT A-00126 Light emitting diode
SRT A-23000 Laser
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Annex D DICOM Controlled Terminology Definitions
Modify the following in PS 3.16 Annex D
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Code Value Code Meaning Definition Notes
111601 Green filter Filter that transmits one third of whitegreen light (green) while blocking the other two thirdscolors, typically centered at 510-540 nm
111602 Red filter Filter that transmits one third of white red light (red) while blocking the other two thirdscolors, typically centered at 630-680 nm
111603 Blue filter Filter that transmits one third of white blue light (blue) while blocking the other two thirdscolors, typically centered at 460-480 nm
Add the following to PS 3.16 Annex D
Code Value Code Meaning Definition Notes
…
111741 Transmission illumination Transmission illumination method for specimen microscopy
111742 Reflection illumination Reflection illumination method for specimen microscopy
111743 Epifluorescence illumination
Epifluorescence illumination method for specimen microscopy
111744 Brightfield illumination Brightfield illumination method for specimen microscopy
111745 Darkfield illumination Darkfield illumination method for specimen microscopy
111746 Oblique illumination Oblique illumination method for specimen microscopy
111747 Phase contrast
illumination
Phase contrast illumination method for specimen microscopy
111748 Differential interference contrast
Differential interference contrast method for specimen microscopy
111749 Total internal reflection fluorescence
Total internal reflection fluorescence method for specimen microscopy
…
121350 Same acquisition at lower resolution
Image of the same target area at lower resolution acquired in the same acquisition process
121354 Imaged container label Image specifically targeting the container label
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