Total Pixel Matrix Origin Sequence Attribute
| Tag | (0048,0008) |
|---|---|
| Type | Required (1) |
| Keyword | TotalPixelMatrixOriginSequence |
| Value Multiplicity | 1 |
| Value Representation | Sequence (SQ) |
Location of pixel 1\1 of the total pixel matrix in the Slide Coordinate System Frame of Reference.
Only a single Item shall be included in this Sequence.
See Section C.8.12.14.1.2 and Section C.8.12.2.1.1 for further explanation.
Section C.8.12.14.1.2
C.8.12.14.1.2 Total Pixel Matrix Origin Sequence and Image Orientation (Slide)
Total Pixel Matrix Origin Sequence (0048,0008) specifies the location of the top leftmost pixel of the pixel matrix, and Image Orientation (Slide) (0048,0102) specifies the direction cosines of the first row and the first column of the pixel matrix, both with respect to the Slide Coordinate System Frame of Reference (see Section C.8.12.2). Although the image acquisition may vary the true row and column orientation at the pixel scale to account for local variation in the physical specimen, this Attribute describes the orientation as if the Pixel Matrix were flat.
Note
Typically, Image Orientation (Slide) will describe only a planar rotation, as the image plane is usually nominally parallel to the slide surface.
Section C.8.12.2.1.1
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.
Note
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The Label of the Slide is presumed to be mounted-on or written-on the Top Surface of the Slide.
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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
Note
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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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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.
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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.
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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.
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Figure C.8-17b. In-vivo microscopy coordinates a) is a front on view b) is top-down view of in-vivo imaging