C.8.12.4 VL Whole Slide Microscopy Image Module

Table C.8.12.4-1 specifies the Attributes that describe the VL Whole Slide Microscopy Image Module.

Table C.8.12.4-1VL WHOLE SLIDE MICROSCOPY IMAGE MODULE ATTRIBUTES

Attribute Name Tag Type Attribute Description
Image Type (0008,0008) 1 Image identification characteristics. See C.8.12.4.1.1 for specialization.
Imaged Volume Width (0048,0001) 1 Width of total imaged volume (distance in the direction of rows in each frame) in mm. See C.8.12.4.1.2
Imaged Volume Height (0048,0002) 1 Height of total imaged volume (distance in the direction of columns in each frame) in mm. See C.8.12.4.1.2
Imaged Volume Depth (0048,0003) 1 Depth of total imaged volume (distance in the Z direction of focal planes) in μm. See C.8.12.4.1.2
Total Pixel Matrix Columns (0048,0006) 1 Total number of columns in pixel matrix; i.e., width of total imaged volume in pixels. See C.8.12.4.1.3
Total Pixel Matrix Rows (0048,0007) 1 Total number of rows in pixel matrix; i.e., height of total imaged volume in pixels. See C.8.12.4.1.3
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 C.8.12.4.1.4 and 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.
Image Orientation (Slide) (0048,0102) 1 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 C.8.12.4.1.4
Samples Per Pixel (0028,0002) 1 Number of samples (color planes) per frame in this image. Enumerated values: 1 or 3. See C.8.12.4.1.5 for further explanation.
Photometric Interpretation (0028,0004) 1 Specifies the intended interpretation of the pixel data. See section C.8.12.4.1.5 for Enumerated Values.
Planar Configuration (0028,0006) 1C Indicates whether the pixel data are sent color-by-plane or color-by-pixel. Required if Samples per Pixel (0028,0002) has a value greater than 1. Enumerated Value: 0 = color-by-pixel
Number of Frames (0028,0008) 1 Number of frames in a multi-frame image. If Image Type (0008,0008) Value 3 is LOCALIZER or LABEL, Enumerated Value is 1.
Bits Allocated (0028,0100) 1 Number of bits allocated for each pixel sample. Enumerated Values: 8, 16
Bits Stored (0028,0101) 1 Number of bits stored for each pixel sample. Enumerated Values: 8, 16
High Bit (0028,0102) 1 Most significant bit for pixel sample data. Enumerated Values: 7, 15
Pixel Representation (0028,0103) 1 Data representation of pixel samples. Enumerated Value: 0 = unsigned integer
Acquisition Datetime (0008,002A) 1 The date and time that the acquisition of data that resulted in this image started.
Acquisition Duration (0018,9073) 1 Duration of the image acquisition in ms.
Lossy Image Compression (0028,2110) 1 Specifies whether an Image has undergone lossy compression. Enumerated Values: 00 - Image has NOT been subjected to lossy compression. 01 - Image has been subjected to lossy compression. See C.7.6.1.1.5
Lossy Image Compression Ratio (0028,2112) 1C See C.7.6.1.1.5 for further explanation. Required if Lossy Image Compression (0028,2110) equals 01.
Lossy Image Compression Method (0028,2114) 1C A label for the lossy compression method(s) that have been applied to this image. See C.7.6.1.1.5 for further explanation. May be multi valued if successive lossy compression steps have been applied; the value order shall correspond to the values of Lossy Image Compression Ratio (0028,2112). Required if Lossy Image Compression (0028,2110) equals 01.
Presentation LUT Shape (2050,0020) 1C Specifies an identity transformation for the Presentation LUT, such that the output of all grayscale transformations defined in the IOD containing this Module are defined to be P-Values. Enumerated Values: IDENTITY - output is in P-Values. Required if Photometric Interpretation (0028,0004) is MONOCHROME2.
Rescale Intercept (0028,1052) 1C The value b in relationship between stored values (SV) and the output units. Output units = m*SV + b. Enumerated value 0 Required if Photometric Interpretation (0028,0004) is MONOCHROME2.
Rescale Slope (0028,1053) 1C m in the equation specified by Rescale Intercept (0028,1052). Enumerated value 1 Required if Photometric Interpretation (0028,0004) is MONOCHROME2.
Volumetric Properties (0008,9206) 1 Indication if geometric manipulations are possible with frames in the SOP Instance. See C.8.16.2.1.2. Enumerated Value: VOLUME - pixels represent the volume specified for the image, and may be geometrically manipulated
Specimen Label in Image (0048,0010) 1 Indicates whether the specimen label is captured in the image. Enumerated Values: YES, NO
Burned In Annotation (0028,0301) 1 Indicates whether or not image contains sufficient burned in annotation to identify the patient. Enumerated Values: YES NO Note: If Specimen Label in Image (0048,0010) value is YES, Burned In Annotation (0028,0301) might be NO if the label includes only a specimen identifier and not patient identifying data.
Focus Method (0048,0011) 1 Method of focusing image Enumerated Values: AUTO – autofocus MANUAL – includes any human adjustment or verification of autofocus
Extended Depth of Field (0048,0012) 1 Image pixels were created through combining of image acquisition at multiple focal planes (focus stacking). Enumerated Values: YES, NO
Number of Focal Planes (0048,0013) 1C Number acquisition focal planes used for extended depth of field. Required if Extended Depth of Field (0048,0012) value is YES
Distance Between Focal Planes (0048,0014) 1C Distance between acquisition focal planes used for extended depth of field, in μm. Required if Extended Depth of Field (0048,0012) value is YES
Acquisition Device Processing Description (0018,1400) 3 Description of visual processing performed on the image prior to exchange. Examples of this processing are: edge enhanced, gamma corrected, convolved (spatially filtered)
Convolution Kernel (0018,1210) 3 Label for convolution kernel used in acquisition device visual processing
Recommended Absent Pixel CIELab Value (0048,0015) 3 A color value with which it is recommended to display the pixels of the Total Pixel Matrix that are not encoded. The units are specified in PCS-Values, and the value is encoded as CIELab. See C.10.7.1.1.

C.8.12.4.1 VL Whole Slide Microscopy Image Attribute Descriptions

C.8.12.4.1.1 Image Type

Image Type (0008,0008) is specified to be Type 1 with the following constraints:

Value 1 shall have a value of ORIGINAL or DERIVED

Value 2 shall have a value of PRIMARY

Value 3 (Image Flavor) shall have the Defined Terms in Table C.8.12.4-2

Table C.8.12.4-2VL WHOLE SLIDE MICROSCOPY IMAGE FLAVORS

LOCALIZER Collected for the purpose of planning or navigating other images.
VOLUME Set of frames that define a regularly sampled volume
LABEL Purpose of image is to capture the slide label; any non-label area captured is incidental to that purpose.

Value 4 (Derived Pixel) shall have the Defined Terms specified in Table C.8.12.4-3.

Table C.8.12.4-3VL WHOLE SLIDE MICROSCOPY DERIVED PIXELS

NONE No derivation of pixels (original)
RESAMPLED Pixels were derived by down sampling a higher resolution image

No additional values shall be present.

C.8.12.4.1.2 Imaged Volume Width, Height, Depth

The full physical extent of the whole slide image target volume is described in the attributes Imaged Volume Width (0048,0001), Imaged Volume Height (0048,0002), and Imaged Volume Depth (0048,0003). These values reflect the maximum extent in these dimensions. There is no requirement that this entire extent is actually encoded in frames of the Image SOP Instance.

The value of Imaged Volume Depth (0048,0003) shall not be 0. If only a single focal plane is imaged, the Imaged Volume Depth may be the optical depth of field as encoded in the Slice Thickness (0018,0050) attribute of the Pixel Measures Functional Group (see C.7.6.16.2.1.1).

C.8.12.4.1.3 Total Pixel Matrix Columns, Rows

Total Pixel Matrix Columns (0048,0006) and Total Pixel Matrix Rows (0048,0007) 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 the Pixel Spacing (0028,0030) attribute of the Pixel Measures Functional Group (see C.7.6.16.2.1.1).

C.8.12.4.1.4 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 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, the Image Orientation (Slide) attribute will describe only a planar rotation, as the image plane is usually nominally parallel to the slide surface.

C.8.12.4.1.5 Photometric Interpretation and Samples per Pixel

Photometric Interpretation (0028,0004) shall be one of these Enumerated Values (see C.7.6.3.1.2):

MONOCHROME2

RGB

YBR_FULL_422

YBR_ICT

YBR_RCT

The value shall be appropriate to the compression transfer syntax used, if any, and shall be MONOCHROME2 or RGB for uncompressed or lossless compressed transfer syntaxes that do not involve color space transformations, YBR_ICT for irreversible JPEG 2000 transfer syntaxes, YBR_RCT for reversible JPEG 2000 transfer syntaxes, and YBR_FULL_422 for other lossy compressed transfer syntaxes.

Note: Future lossless and lossy transfer syntaxes may lead to the need for new definitions and choices for Photometric Interpretation. The Enumerated Values may therefore be extended with additional Photometric Interpretation values directly associated with new transfer syntaxes that are negotiated, and hence do not render existing implementations non-conformant.

Multi-spectral images may be encoded as a single wavelength band (color) in each frame using MONOCHROME2, or with up to three bands in each frame using one of the color Photometric Interpretations.

Samples per Pixel (0028,0002) shall be 1 for MONOCHROME2, and 3 otherwise.