Z Offset in Slide Coordinate System Attribute
| Tag | (0040,074A) |
|---|---|
| Type | Required, Empty if Unknown (2) |
| Keyword | ZOffsetInSlideCoordinateSystem |
| Value Multiplicity | 1 |
| Value Representation | Decimal String (DS) |
The Z offset in µm from the image substrate reference plane (i.e., utilized surface of a glass slide).
Note
The use of units of microns is inconsistent with the use of millimeters for Point Coordinates Data (0066,0016), Double Point Coordinates Data (0066,0022) and Common Z Coordinate Value (006A,0010) in the Section C.37.1.2 Microscopy Bulk Simple Annotations Module.
Section C.37.1.2 Microscopy Bulk Simple Annotations Module
C.37.1.2 Microscopy Bulk Simple Annotations Module
Table C.37.1-2 specifies the Attributes of the Microscopy Bulk Simple Annotations Module, which describe the Microscopy Bulk Simple Annotations.
Table C.37.1-2. Microscopy Bulk Simple Annotations Module Attributes
|
Attribute Name |
Tag |
Type |
Attribute Description |
|---|---|---|---|
|
Include Table 10-12 “Content Identification Macro Attributes” |
|||
|
Content Date |
(0008,0023) |
1 |
The date the content creation started. |
|
Content Time |
(0008,0033) |
1 |
The time the content creation started. |
|
Annotation Coordinate Type |
(006A,0001) |
1 |
Whether coordinates are image-relative (2D) or volume-relative (3D). Enumerated Values:
|
|
Pixel Origin Interpretation |
(0048,0301) |
1C |
For image-relative coordinates, specifies whether coordinates are to be interpreted relative to the individual frame pixel origins, or relative to the Total Pixel Matrix origin (see Section C.8.12.4.1.4). Required if Annotation Coordinate Type (006A,0001) is 2D. Enumerated Values:
NoteThe use of the term "VOLUME" to refer to the Total Pixel Matrix is historical and inherited from Presentation States, and does not refer to 3D coordinates. |
|
Referenced Image Sequence |
(0008,1140) |
1C |
The image to which this Annotation object applies. Only a single Item shall be included in this Sequence. Required if Annotation Coordinate Type (006A,0001) is 2D. May be present otherwise. |
|
>Include Table 10-3 “Image SOP Instance Reference Macro Attributes” |
|||
|
Annotation Group Sequence |
(006A,0002) |
1 |
Groups of Annotations sharing common characteristics, such as graphic type, properties or measurements. One or more Items shall be included in this Sequence. |
|
>Annotation Group Number |
(0040,A180) |
1 |
Identification number of the Annotation Group. Uniquely identifies a Annotation Group within this SOP Instance. Shall start at a value of 1, and increase monotonically by 1. |
|
>Annotation Group UID |
(006A,0003) |
1 |
Unique identifier of the Annotation Group. |
|
>Annotation Group Label |
(006A,0005) |
1 |
User-defined label identifying this Annotation Group. This may be the same as Code Meaning (0008,0104) of Annotation Property Type Code Sequence (006A,000A). |
|
>Annotation Group Description |
(006A,0006) |
3 |
User-defined description for this Annotation Group. |
|
>Annotation Group Generation Type |
(006A,0007) |
1 |
Type of algorithm used to generate the Annotations. Enumerated Values:
|
|
>Annotation Group Algorithm Identification Sequence |
(006A,0008) |
1C |
The algorithms used to create the Annotations in this group. One or more Items shall be included in this Sequence. Required if Annotation Generation Type (006A,0007) is AUTOMATIC or SEMIAUTOMATIC. |
|
>>Include Table 10-19 “Algorithm Identification Macro Attributes”. |
|||
|
>Include Table 10-7b “Multiple Site General Anatomy Optional Macro Attributes” |
May not be necessary if the anatomy is implicit in the Annotation Property Type Code Sequence (006A,000A). More than one Item in Anatomic Region Sequence (0008,2218) may be used when a region of interest spans multiple anatomical locations and there is not a single pre-coordinated code describing the combination of locations. There is no requirement that the multiple locations be contiguous. |
||
|
>Annotation Property Category Code Sequence |
(006A,0009) |
1 |
Sequence defining the general category of the property the Annotation Group represents. Only a single Item shall be included in this Sequence. |
|
>Annotation Property Type Code Sequence |
(006A,000A) |
1 |
Sequence defining the specific property the Annotation Group represents. Only a single Item shall be included in this Sequence. |
|
>>Annotation Property Type Modifier Code Sequence |
(006A,000B) |
3 |
Sequence defining the modifier of the property type of this Annotation Group. One or more Items are permitted in this Sequence. |
|
>>>Include Table 8.8-1 “Code Sequence Macro Attributes” |
No Baseline CID is defined. |
||
|
>Number of Annotations |
(006A,000C) |
1 |
The number of Annotations in this Annotation Group. Each point, polyline or polygon, ellipse or rectangle is counted as one Annotation. |
|
>Graphic Type |
(0070,0023) |
1 |
The shape of the Annotations in this Annotation Group. See Section C.37.1.2.1.1. Enumerated Values:
NoteIndividual Annotations in the same group are not required to be in the same plane. |
|
>Annotation Applies to All Optical Paths |
(006A,000D) |
1 |
Whether the Annotations in this Annotation Group apply to all the optical paths within the corresponding images. Enumerated Values:
|
|
>Referenced Optical Path Identifier |
(006A,000E) |
1C |
Identifies one or more optical paths to which this Annotation applies. Refers to the same value in Optical Path Identifier (0048,0106) within the Optical Path Sequence (0048,0105) in the images to which this Annotation applies. More than one value may be present if the Annotations apply to more than one (but not all) Optical Paths. Required if Annotation Applies to All Optical Paths (006A,000D) is NO. |
|
>Annotation Applies to All Z Planes |
(006A,000F) |
1C |
Whether the Annotations in this Annotation Group apply to the full thickness of the tissue on the slide. I.e., they are applicable regardless of the focal plane, in the case that images were acquired with multiple focal planes (Z-stacks). Enumerated Values:
NoteWhen the value is NO, the Z plane will be specified either in Common Z Coordinate Value (006A,0010) if all the coordinates are in the same Z plane(s), or in Point Coordinates Data (0066,0016) or Double Point Coordinates Data (0066,0022) if not. Required if Annotation Coordinate Type (006A,0001) is 3D. |
|
>Common Z Coordinate Value |
(006A,0010) |
1C |
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). NoteThis 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. |
|
>Point Coordinates Data |
(0066,0016) |
1C |
The coordinates of one or more points that define the Annotations (whether single points or polygons), encoded in (X, Y) or (X, Y, Z) order. Required if Double Point Coordinates Data (0066,0022) is not present. For each point, two coordinates (X, Y) shall be encoded if Common Z Coordinate Value (006A,0010) is present, otherwise three coordinates (X, Y, Z) shall be encoded. See Section C.37.1.2.1.1. |
|
>Double Point Coordinates Data |
(0066,0022) |
1C |
The coordinates of one or more points that define the Annotations (whether single points or polygons), encoded in (X, Y) or (X, Y, Z) order. Required if Point Coordinates Data (0066,0016) is not present. For each point, two coordinates (X, Y) shall be encoded if Common Z Coordinate Value (006A,0010) is present, otherwise three coordinates (X, Y, Z) shall be encoded. See Section C.37.1.2.1.1. |
|
>Long Primitive Point Index List |
(0066,0040) |
1C |
A list of point indices. See Section C.37.1.2.1.1. Required if Graphic Type (0070,0023) is POLYLINE or POLYGON. |
|
>Recommended Display CIELab Value |
(0062,000D) |
3 |
Default triplet value in which it is recommended that the Annotation Group be rendered. The units are specified in PCS-Values, and the value is encoded as CIELab. See Section C.10.7.1.1. |
|
>Measurements Sequence |
(0066,0121) |
3 |
Measurements for some or all Annotations in the Annotation Group. Each Item describes one type of measurement. See Section C.37.1.2.1.2. One or more Items are permitted in this Sequence. |
|
>>Concept Name Code Sequence |
(0040,A043) |
1 |
Defines the type of measurement stored in this Item. Only a single Item shall be included in this Sequence. |
|
>>>Include Table 8.8-1 “Code Sequence Macro Attributes” |
|||
|
>>Measurement Units Code Sequence |
(0040,08EA) |
1 |
Units of measurement for the value in this Item. Only a single Item shall be included in this Sequence. |
|
>>>Include Table 8.8-1 “Code Sequence Macro Attributes” |
|||
|
>>Measurement Values Sequence |
(0066,0132) |
1 |
The measurement values for the Annotation Group. One or more Items shall be included in this Sequence. |
|
>>>Floating Point Values |
(0066,0125) |
1 |
Measurement values for Annotations stored in this Annotation Group. If Annotation Index List (006A,0011) is present, measurement values are stored for a subset of Annotations, and the number of values shall match the number and order of indices in Annotation Index List (006A,0011). If Annotation Index List (006A,0011) is absent, measurement values are stored for every Annotation in Long Primitive Point Index List (0066,0040), if present, and the number of values shall match the number and order of Annotations in Long Primitive Point Index List (0066,0040) . If Annotation Index List (006A,0011) and Long Primitive Point Index List (0066,0040) are absent, measurement values are stored for every Annotation stored in Point Coordinates Data (0066,0016) or Double Point Coordinates Data (0066,0022), and the number of values shall match thevalue of Number of Annotations (006A,000C). See Section C.37.1.2.1.2. |
|
>>>Annotation Index List |
(006A,0011) |
1C |
List of indices referencing Annotations identified in Long Primitive Point Index List (0066,0040) or successive points stored in Point Coordinates Data (0066,0016) or Double Point Coordinates Data (0066,0022) for which measurement values shall be stored. Required if Measurement Values stored in Floating Point Values (0066,0125) are associated with only a subset of Annotations. See Section C.37.1.2.1.2. |
C.37.1.2.1 Microscopy Bulk Simple Annotations Module Attribute Descriptions
C.37.1.2.1.1 Type, Points, Polygons, Parameterized and Rotated Shapes and Indices
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).
Note
-
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.
Note
-
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.
Note
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).
Note
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).
Note
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).
C.37.1.2.1.2 Measurements
For each Annotation Group, optionally one or more measurements may be defined, either for every Annotation or a subset of Annotations. Measurements are described by coded type and unit.
When there is a measurement for every Annotation, then Floating Point Values (0066,0125) contains the corresponding values for each of the Annotations. When there are measurements for only a subset of Annotations, then Floating Point Values (0066,0125) contains measurement values for the Annotations that are referenced in Annotation Index List (006A,0011).
More than one Measurements Sequence (0066,0121) Item may be used, for example to encode different types of measurements, or to encode different components of a measurement that is a tuple.
Within one Annotation Group the types of measurements are the same for all Annotations within that group.