Tag | (006A,0010) |
---|---|
Type | Conditionally Required (1C) |
Keyword | CommonZCoordinateValue |
Value Multiplicity | 1-n |
Value Representation | Double (FD) |
The Z coordinate(s) common to all points in Point Coordinates Data (0066,0016) or Double Point Coordinates Data (0066,0022), in mm in the Slide Coordinate System (Section C.8.12.2.1.1) associated with the Frame of Reference.
More than one value may be present if the Annotations apply to more than one (but not all) Z planes.
Required if Annotation Coordinate Type (006A,0001) is 3D, and all points in Point Coordinates Data (0066,0016) or Double Point Coordinates Data (0066,0022) are in the same Z plane(s).
This requirement means that it is mandatory to factor out the commonality, i.e., it is not permitted to send Point Coordinates Data (0066,0016) or Double Point Coordinates Data (0066,0022) with (X, Y, Z) triplets where all the Z values are the same. For Annotations of images that only have a single Z plane, or where all the points in an Annotation Group are coplanar and in the same Z plane, this condition will always be satisfied. Annotations in different Z planes can be separated into separate Annotation Groups in order to allow this condition to be satisfied, but using separate Annotation Groups is not required.
See Section C.37.1.2.1.1.
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.
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.
The Label of the Slide is presumed to be mounted-on or written-on the Top Surface of the Slide.
Specification of the mechanical form, function, or tolerances of the Microscope are outside the scope of this Standard.
Figure C.8-16 and Figure C.8-16b depict 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.
Figure C.8-16. Reference Slide Orientation - Ex-vivo imaging - slide contains label
Figure C.8-16b. Reference Slide Orientation - Ex-vivo imaging - slide does not contain label
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.
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.
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.
The origin of a Frame of Reference is arbitrary (see Section 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 Offset in Slide Coordinate System (0040,072A) shall increase from the Origin toward the Right Edge in Reference Slide Orientation. The Y Offset in Slide Coordinate System (0040,073A) shall increase from the Origin toward the Label Edge or Top Edge (in the absence of a label) in Reference Slide Orientation. The Z Offset in Slide Coordinate System (0040,074A) 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.
Figure C.8-17. Z-Axis Center Point Location, View From Right Edge of Slide
In-vivo imaging uses a Cartesian, orthogonal, right-handed coordinate system. This coordinate system is depicted in Figure C.8-17b. The Y-axis is oriented from the nominal bottom of the microscope to the nominal top of the microscope. The X-axis is oriented from nominal left of the microscope to the nominal right of the microscope. The Z-axis is oriented from the subject towards the microscope.
Figure C.8-17b. In-vivo microscopy coordinates a) is a front on view b) is top-down view of in-vivo imaging
All the Annotations in a single Item of Annotation Group Sequence (006A,0002) share the same value for Graphic Type (0070,0023).
If Annotation Coordinate Type (006A,0001) is 2D, then the coordinates are interpreted as image-relative, either relative to an individual frame or the Total Pixel Matrix, with units of pixels, as defined in Section C.10.4 Displayed Area Module. If Pixel Origin Interpretation (0048,0301) is FRAME, then a single frame of a single image shall be specified in Referenced Image Sequence (0008,1140). If Pixel Origin Interpretation (0048,0301) is VOLUME, then a single image shall be specified in Referenced Image Sequence (0008,1140) without a subset of frames designated, and the coordinates are relative to the Total Pixel Matrix of that image. The referenced image shall not be an instance of a Concatenation; i.e., in the case of Concatenations, references shall be relative to the SOP Instance UID of Concatenation Source (0020,0242).
The referenced image need not be any particular resolution layer of a WSI pyramid. I.e., it may or may not be the highest resolution layer. The user may annotate images that are not at the highest resolution, but such Annotations may be projected onto any resolution layer that is available (or computed). If the referenced image is no longer stored or accessible, the ability to project the Annotations onto other layers may be lost.
A reference to a single frame means that all Annotations in this instance are on that frame; no mechanism is provided to span frames, or to specify more than one frame.
If Annotation Coordinate Type (006A,0001) is 3D, then the X, Y and Z coordinates are interpreted as volume relative, with units of mm, in the Cartesian space defined by the Frame of Reference UID.
A single referenced image may be specified even if Annotation Coordinate Type (006A,0001) is 3D. It need not be any particular resolution layer of a WSI pyramid, but may be interpreted as a suitable layer on which to render, select from or otherwise apply the Annotation. In particular, it may not be the highest resolution layer. Regardless, the Annotations are applicable to any image in the same Frame of Reference.
The use of millimeters as the unit for the Z coordinates is inconsistent with the use of microns for the Z Offset in Slide Coordinate System (0040,074A) in the Section C.8.12.2 Slide Coordinates Module.
If the Annotations are points, then
Graphic Type (0070,0023) shall have a value of POINT.
All the points in the group shall be encoded in Point Coordinates Data (0066,0016) or Double Point Coordinates Data (0066,0022), concatenated one after another, with Z factored out into Common Z Coordinate Value (006A,0010), if common.
Long Primitive Point Index List (0066,0040) shall not be present, because there is no need for a separate index of each Annotation.
Number of Annotations (006A,000C) will contain the number of points, which shall also be the number of coordinate tuples in Point Coordinates Data (0066,0016) or Double Point Coordinates Data (0066,0022).
If the Annotations are open polylines, then
Graphic Type (0070,0023) shall have a value of POLYLINE.
The points of each polyline shall be encoded in Point Coordinates Data (0066,0016) or Double Point Coordinates Data (0066,0022), concatenated one after another, with Z factored out into Common Z Coordinate Value (006A,0010), if common.
The order of the encoded points is from the first point to the last point of the polyline.
The index in Point Coordinates Data (0066,0016) or Double Point Coordinates Data (0066,0022) of each successive polyline is encoded in Long Primitive Point Index List (0066,0040), which shall contain Number of Annotations (006A,000C) values.
If the Annotations are closed polygons, then
Graphic Type (0070,0023) shall have a value of POLYGON.
The points of each polygon shall be encoded in Point Coordinates Data (0066,0016) or Double Point Coordinates Data (0066,0022), concatenated one after another, with Z factored out into Common Z Coordinate Value (006A,0010), if common.
The order of the encoded points is from the first point to the last point of the polygon. The first point and the last point shall not be the same, but rather they are implicitly joined to close the polygon.
The index in Point Coordinates Data (0066,0016) or Double Point Coordinates Data (0066,0022) of each successive polygon is encoded in Long Primitive Point Index List (0066,0040), which shall contain Number of Annotations (006A,000C) values.
This closed polygon representation differs from that used in Presentation States (Section C.10.5.1.2 Graphic Data and Graphic Type) and Structured Reports (Section C.18.6.1 Spatial Coordinates Macro Attribute Descriptions and Section C.18.9.1 3D Spatial Coordinates Macro Attribute Descriptions), none of which are implicitly closed, and required replication of the first point as the last point.
If the Annotations are circles or ellipses, then
Graphic Type (0070,0023) shall have a value of ELLIPSE.
The end points of the major and minor axes of the ellipses in the group shall be encoded in Point Coordinates Data (0066,0016) or Double Point Coordinates Data (0066,0022), with Z factored out into Common Z Coordinate Value (006A,0010) if common.
Long Primitive Point Index List (0066,0040) shall not be present, because the index of each Annotation can be computed. Number of Annotations (006A,000C) will contain the number of ellipses, which shall also be one quarter of the number of coordinate tuples in Point Coordinates Data (0066,0016) or Double Point Coordinates Data (0066,0022).
If the length of the major and minor axes are the same, then the ellipse is a circle; a simpler (e.g., 2 point) encoding of a circle is not defined, since the plane of the circle would be unspecified without a third point.
If the Annotations are squares or rectangles, then
Graphic Type (0070,0023) shall have a value of RECTANGLE.
All the corner points of the rectangles in the group shall be encoded in Point Coordinates Data (0066,0016) or Double Point Coordinates Data (0066,0022), with Z factored out into Common Z Coordinate Value (006A,0010) if common.
Long Primitive Point Index List (0066,0040) shall not be present, because the index of each Annotation can be computed. Number of Annotations (006A,000C) will contain the number of rectangles, which shall also be one quarter of the number of coordinate tuples in Point Coordinates Data (0066,0016) or Double Point Coordinates Data (0066,0022).
If the lengths of the perpendicular edges are the same, then the rectangle is a square. This rectangle representation is the same as if the rectangle were encoded as an implicitly closed polygon, except that the number of points is fixed and Long Primitive Point Index List (0066,0040) is absent. A simpler (e.g., 2 point TLHC, BRHC) encoding of a rectangle is not defined, since the plane of the rectangle would then be unspecified without a third point.
The index used in Long Primitive Point Index List (0066,0040) of the first value of the first coordinate tuple in Point Coordinates Data (0066,0016) or Double Point Coordinates Data (0066,0022) shall be 1.
The polylines and polygons encoded in Point Coordinates Data (0066,0016) or Double Point Coordinates Data (0066,0022) shall be in the same order as Long Primitive Point Index List (0066,0040). I.e., the values of Long Primitive Point Index List (0066,0040) are strictly increasing.
Open polylines and implicitly closed polygons shall have their vertices encoded in Point Coordinates Data (0066,0016) or Double Point Coordinates Data (0066,0022) in clockwise winding order when viewed from the top surface of the slide towards the bottom, per Section C.8.12.2.1 Slide Coordinates Module Attribute Descriptions. The line segments shall not cross (i.e., shall be simple polygons, not complex polygons), and shall not contain holes (i.e., the keyhole technique described for RT Structure Sets (Section C.8.8.6.3 Representing Inner and Outer Contours), shall not be used).
The plane of the coplanar points is not required to correspond to an image plane or be parallel to the slide surface; the points are only required to be coplanar in a geometric sense (i.e., they need not all have the same Z coordinate value).