C.8.12.14 Microscope Slide Layer Tile Organization Module

C.8.12.14 Microscope Slide Layer Tile Organization Module (Current)
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Table C.8.12.14-1 specifies the Attributes of the Microscope Slide Layer Tile Organization Module, which describe the logical and physical organization of the tiles within a single resolution layer encoded as a tiled Image, such as that of a Multi-Resolution Pyramid.

Table C.8.12.14-1. Microscope Slide Layer Tile Organization Module Attributes

Attribute Name	Tag	Type	Attribute Description
Total Pixel Matrix Columns	(0048,0006)	1	Total number of columns in pixel matrix; i.e., width of total imaged volume in pixels. See Section C.8.12.14.1.1
Total Pixel Matrix Rows	(0048,0007)	1	Total number of rows in pixel matrix; i.e., height of total imaged volume in pixels. See Section C.8.12.14.1.1
Total Pixel Matrix Focal Planes	(0048,0303)	1C	Total number of focal planes (Z locations) in the pixel matrix; i.e., depth of total imaged volume in pixels. See Section C.8.12.14.1.1 Required if Dimension Organization Type (0020,9311) is present with a value of TILED_FULL. May be present otherwise. Note Total Pixel Matrix Focal Planes (0048,0303) describes the number of focal planes separately encoded, and is distinct from Number of Focal Planes (0048,0013), which describes in what manner different focal planes were combined into a single encoded plane (focus stacking).
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 Section C.8.12.14.1.2 and 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.
>Y Offset in Slide Coordinate System	(0040,073A)	1	The Y offset in millimeters from the Origin of the Slide Coordinate System.
>Z Offset in Slide Coordinate System	(0040,074A)	1C	The Z offset in µm from the image substrate reference plane (i.e., utilized surface of a glass slide). Required if the Z offset is not zero. May be present otherwise. Note The conditional requirement is used because, historically, this Attribute was not present.
Image Orientation (Slide)	(0048,0102)	1C	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 Section C.8.12.14.1.2. Required if Plane Position (Slide) Sequence (0048,021A) is present within a Functional Group Sequence or Dimension Organization Type (0020,9311) is present with a value of TILED_FULL. May be present otherwise. Note This condition will always be satisfied when this Module is included in the Whole Slide Microscopy Image IOD.

C.8.12.14.1 Microscope Slide Layer Tile Organization Module Attribute Descriptions

C.8.12.14.1.1 Total Pixel Matrix Columns, Rows, Focal Planes

Total Pixel Matrix Columns (0048,0006), Total Pixel Matrix Rows (0048,0007) and Total Pixel Matrix Focal Planes (0048,0303) 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 Pixel Spacing (0028,0030) of the Pixel Measures Functional Group (see Section C.7.6.16.2.1), such as when Dimension Organization Type (0020,9311) is present with a value of TILED_FULL.

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.

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