1. Supplement 145 Whole Slide Imaging – background and design decisions
Harry Solomon GE Healthcare

2. DICOM Basics

3. DICOM Image Information Object Definition
Patient Name
Patient ID
Patient Sex
Patient Birthdate
DICOM Composite
Information Model
Hierarchy
Patient
Module
Patient
Information
Study Unique ID
Accession Number
Study Date/Time
Study Description
Referring MD
General
Study
Module
Patient
Study
Module
Study
Information
General
Series
Module
Frame of
Reference
Module
General
Equipment
Module
Rows/Columns
Bits per Pixel
Photometric
Series
Information
General
Image
Module
Image
Plane
Module
Contrast/
Bolus
Module
Image
Pixel
Module
Image
(Instance)
Information
Modality
Image
Module
Multi-
frame
Module
VOI
LUT
Module …
SOP
Common
Module
Dwight Simon

4. Value Represen- tation Study Instance Unique Identifier (0020,000D)
Data Element Encoding
Attributes are the logical concepts associated with an information entity
Data elements are how attributes are encoded in an information object
Data Set
order of transmission
Data Elem.
Data Elem.
Data Elem.
Data Elem.
Data Element
Value Represen- tation
Similar to TIFF
Value
Tag
Value Field
Length
optional field - dependent on
negotiated Transfer Syntax
Dhex UI
26hex
Study Instance Unique Identifier (0020,000D)
Instance UID encoded as “dotted decimal”

5. Part of a DICOM object Tags in increasing numeric order
Patient
Information
Study
Series
Image
(Instance)
(0008,0005) CS 30
ISO 2022 IR 13\ISO 2022 IR 87
(0008,0008) 22
ORIGINAL\PRIMARY\AXIAL
(0008,0016) UI 26
(0008,0018) 58
(0008,0020) DA 8
(0008,0021)
(0008,0022)
(0008,0023)
(0008,0030) TM 10
(0008,0031)
(0008,0032)
(0008,0033)
(0008,0050) SH
(0008,0060) 2 CT
(0008,0070) LO
TOSHIBA …
(7FE0,0010) OW
524288
ff ff ff ff 00 0f 4c 4a
Tags in increasing numeric order
Value length always an even number
Attributes related to modules and information model levels all jumbled up

6. Attributes
Logical concepts in the description of an Information Entity
May have 0, 1 or many Values
0 (empty) means the creating application doesn’t know the value of the attribute, e.g. Accession Number (0008,0050)
Multi-value example: Specific Character Set (0008,0005)
Value Multiplicity (VM) specified in Part 6 (possibly further constrained in Part 3)
Attribute value will be a complex data structure for a Sequence attribute

7. Sequence Attributes and Items
Sequence attribute has a “value” of a structure of subsidiary attributes
Sequence Attribute name typically includes word “Sequence”
Subsidiary attributes specified in Part 3 with > character
Each instantiated set of attributes is a Sequence Item
Number of allowed Items specified in Part 3
For editorial convenience the attributes of a Sequence are often documented in a separate Table as a Macro
Include ‘x Macro’ Table m-n
Facilitates reuse of structure in other sequence attributes

8. Example: Scheduled Protocol Code Sequence attribute

9. Scheduled Protocol Code Sequence attribute
(0040,0008)
>Code Value
(0008,0100)
>Coding Scheme Version
(0008,0103)
>Coding Scheme Designator
(0008,0102)
>Code Meaning
(0008,0104)
>Protocol Context Sequence
(0040,0440)
>>Value Type
(0040,A040)
>>Concept Name Code Sequence
(0040,A043)
>>>Code Value
>>>Coding Scheme Designator
>>>Coding Scheme Version
>>>Code Meaning
>>DateTime
(0040,A120)
>>Person Name
(0040,A123)
>>Text Value
(0040,A160)
>>Concept Code Sequence
(0040,A168) …
>>Content Item Modifier Sequence
(0040,0441)
>>>Value Type
>>>Concept Name Code Sequence
>>>>Code Value
>>>>Coding Scheme Designator

10. Sequence attribute encoding
Sequence Items are the “values” of Sequence attributes
Structure placed in the Data Element Value Field
Item structure is a “nested data set” of attributes
Attributes in each Item in tag order
Item “wrapped” using special data elements specified in Part 5
Sequence attributes and wrappers may have an “undefined length” flag
Length of Sequence or Item terminated by explicit Delimiter data elements
May be “undefined length”
Sequence Data Element
Value Represen- tation SQ
Value
Tag
Value Field
Length
Item
Introducer
Attribute 1
Attribute 2
Item
Delimiter
Item
Introducer
Attribute 1
Attribute 2
Item
Delimiter
Sequence
Delimiter
Specifies length of Item, or may say “undefined length”
Required if “undefined length” Item
Required if “undefined length” Sequence Attribute

11. Image Compression
Pixel data can be monochrome, color (RGB or YCbCr), or palette color (monochrome colorized through LUT)
No definitions yet for hyperspectral, but it has been discussed
Pixel data can be ‘native DICOM’ (with color by-plane or by-pixel)
Pixel data can be compressed using standard compression schemes, and compressed stream put in pixel data element
JPEG, JPEG-LS, JPEG2000 (each lossy or lossless)
MPEG2
Run-Length Encoding (Packbits)
Private compression schemes can also be used

12. Compressed Image Encoding
Uses structure similar to Sequence attribute
Allows “undefined length” attribute – eliminates 232 byte limitation
1st Item is ‘Basic Offset Table’ - pointers to individual frames of a multi-frame image (optional)
JPEG and JPEG2000Part1 encode each frame of a multi-frame image in a separate Encapsulated Stream Fragment
JPEG2000Part2 (multicomponent) allows arbitrary mapping of frames to stream fragments to allow component collections (inter-frame compression)
May be “undefined length
Pixel Data Element
Value Represen- tation OB
Tag
Value
Value Field
(7FE0,0010)
Length
Item
Introducer
Basic Offset
Table
Item
Introducer
Encapsulated Stream
Fragment 1
Item
Introducer
Encapsulated Stream
Fragment 2
Sequence
Delimiter
Specifies length of
Basic Offset Table
Specifies length of
Stream Fragment
Required if “undefined length” Pixel Data Attribute

13. Multiframe Images

14. Enhanced Multi-frame paradigm
Basic concept used for all new multiframe IODs
MR (Image and Spectroscopy), CT, XA, US, PET
Multi-frame object to support image studies
Dynamic image header supports functional or acquisition attributes changing during scan
Dimensions allow multiple views of data
File size flexibility through concatenations

15. Single-frame to MultiFrame
N Objects, N Headers
N Frames, One Header
Fixed Header
Per-frame header
Dimension data
Pixel data

16. Functional Groups and the Per-Frame Header

17. Functional Groups Collection of set of closely related attributes
A “mini Module”
Structured as a sequence of (usually 1) item under a main Sequence attribute
Invoked as a ‘Macro’ in either Shared Functional Groups Sequence or Per-Frame Functional Groups Sequence
Keeps items together in encoding under the main Sequence attribute

18. Dimensions – properties that may change
echo
cardiac phase
b-value
orientation
time
position
volume
time

19. Multi-phase / Multi-slice
Phase (Time) Position Index 1 2 3
Slice Order for phase 1
Phase order for slice 2 6 5 4 3 2 1
Physical Location
(Stack) Index 6 5 4 3 2 1 6 5 4 3 2 1
This is an example of a stack imaged 3 times.
There is only 1 stack in this example.
The in-stack positions indexes for phases 1,2 and 3 refer to the same slice.
The temporal position index is a logical index and while each frame within a temporal set may have been imaged at a slightly different time the set is still organized by a single time index.
Frame number 1-6
Frame number 13-18
Frame number 7-12
Image frames can be sorted/displayed independent of encoded frame order

20. Concatenations What is a concatenation? Why? set of image objects
in the same series
with the same dimension indexes
uniquely identified with a Concatenation UID (0020,9161)
“contained” image objects must have the same Instance Number
Why?
file system limits – e.g., 600 MB CD-R
pseudo real-time transfer of a stream of images
workstation needs to post process images in near real time to figure out when the scan is to be terminated
Describe why we need concatenations – real world considerations.
Describe the rules behind a concatenation

21. Concatenations Legend:
Pixel data (not on scale)
Dimension data (not on scale)
Per-frame header
Fixed Header
Point out that the top picture is an acquisition that is too big for some system limit.
Show how a logical frame set would be divided into smaller ones – based on the different colored boxes.
An object may be split up into two or more SOP Instances, using the same concatenation UID

22. Image Retrieval

23. DICOM Query/Retrieve
Allows a system to query another system for a list of available images (query) Also allows a system to request another system to send images (retrieve)
Query Request
PACS
Query/Retrieve
SCP
Query/Retrieve
SCU
Workstation
Query Match(es)
Retrieve Request
Image(s) Send
Store Response(s)
Retrieve Response

24. Hierarchical Query DICOM query is not a full SQL-type feature
Limited attributes, no Join capability
Directed toward production imaging department requirements
Hierarchical data structure
(Patient), Study, Series, Image levels
Patient attributes typically subsumed in Study level
Query at any level requires specification of unique entity at each higher level

25. Typical Hierarchical Query
Level: STUDY
Patient ID: D73001
Date:
Query/Retrieve
SCU
Workstation
PACS
Query/Retrieve
SCP
Study ID:
Study UID:
Patient ID: D73001
Date:
Study ID:
Study UID:
Date:
Study ID:
Study UID:
Date:
Level: SERIES
Study UID:
Study UID:
Series Num: 2
Series UID:
Modality: CT
Series Num: 1
Series UID:
Level: IMAGE
Study UID:
Series UID:
Study UID:
Series UID:
Image UID:
Image UID:
Image UID:

26. Classical Hierarchical Retrieve
Retrieve can be at any hierarchical level
(Patient), Study, Series, Image
Retrieve at any level requires unique ID of entity at each higher level
Object transfer can be on separate Association (C-MOVE) or on same Association (C-GET)
C-MOVE object transfer can be directed to third party
Examples:
Retrieve all objects under Study UID
Retrieve all objects under Study UID / Series UID
Retrieve single object Study UID / Series UID / Instance UID
Retrieved objects sent and confirmed as wholes

27. Interactive JPIP Retrieve
Image Store SCU and SCP can negotiate a JPEG 2000 Interactive Protocol (JPIP) Transfer Syntax
Image header (i.e., entire object minus pixel data) transferred and confirmed as usual
Pixel data replaced by URL to JPIP service for this image
Limitations
Pixel data must be in JPEG 2000 format
Storage Commitment not allowed
Duration of availability of JPIP not specified or guaranteed
Capabilities
Retrieve subset of image (ROI)
Retrieve at a lower resolution (e.g., for quick navigation)

28. Frame-based retrieve New in 2009 Supplement 119
Retrieve subset of frames from a multi-frame image
Selected frames of a volumetric stack (ROI)
Decimated volume (e.g., every 10th slice)
Single dimension of a multi-dimensional image
Time snippet of motion image (video)
SCU & SCP negotiate “Instance Root Retrieve” SOP Class
SCU specifies selected frames or time interval
SCP creates new multi-frame image with derivation attributes
Frame Derivation Module and Contributing Equipment Sequence
Correct subset of Functional Group Sequence Items

29. Vocabulary and Structured Reporting

30. Vocabulary-intensive messaging
There’s a lot of things we want to say about imaging that cannot be pre-defined in fixed DICOM attributes
E.g., specimen processing
How do we define message attributes to handle what we need to say?

31. Name-value pairs Why would we want to do this? 00180015 ABDOMENPELVIS
= Body Part Examined
ABDOMENPELVIS
< BodyPartExamined “ABDOMENPELVIS” />
<el> <name “BodyPartExamined” />
<value “ABDOMENPELVIS” /> </el>
<el>
<name code= system=DICOM meaning=“Body Part Examined” /> <value code=R-FAB57 system=SNOMED meaning=“Abdomen and pelvis” />
</el>
Why would we want to do this?

32. External coded/concept terminologies
Flexibility and extensibility
Leverage externally defined/maintained concepts
Semantic rigor through referenced dictionary/ ontology
General structure – higher layer of abstraction
Allows generalized messaging applications
Shared vocabulary across disparate systems

33. SNOMED Systematized Nomenclature of Medicine
Most comprehensive clinical healthcare terminology
375,000 concepts; 900,000 relationships between concepts
Multi-hierarchically organized
Primary external vocabulary system for DICOM
Anatomy
Procedures (including radiographic views and methods)
Clinical findings
Originally developed by the College of American Pathologists, now managed by an international consortium of governmental agencies (IHTSDO)

34. LOINC Logical Observation Identifier Names and Codes
Standard coding system for laboratory and clinical observations
Hosted by Regenstrief Institute
Supported by National Library of Medicine
Particularly focused on names of laboratory and clinical tests
50,000 codes; over 275,000 relationships
Major external code system for DICOM and HL7

35. Code Sequences DICOM Part 3
“Triplet coding” : code value, scheme, meaning
(version seldom used)

36. Context Groups (Value Sets)
DICOM Part 3
DICOM Part 16

37. Content Items
Generic Name:Value pair using external coding for Name concept
Encoded as Item in Sequence attributes:
Acquisition Context Sequence (in image IODs)
Protocol Context Sequence (in Modality Worklist)
Content Sequence (in Structured Reporting IODs)
Specimen Preparation Step Sequence (in Specimen Module)
DateTime Value (0040,A120)
Person Name Value (0040,A123)
Referenced SOP Sequence (0008,1199)
Text Value (0040,A160)
UID Value (0040,A124)
Content Item
SOP Class UID (0008,0050)
SOP Instance UID (0008,0055)
Concept Name
Sequence (0040,A043)
Value Type
(0040,A040)
Concept Value
Sequence (0040,A168)
Numeric Value
(0040,A30A)
Measurement Units Sequence (0040,08EA)
Code (0008,0100)
Scheme (0008,0102)
Meaning (0008,0104)
Code (0008,0100)
Scheme (0008,0102)
Meaning (0008,0104)
Code (0008,0100)
Scheme (0008,0102)
Meaning (0008,0104)

38. HL7 v3 ActClass equivalent
Templates
Structure for Content Items - like Modules are a structure for Attributes Specified in DICOM Part 16
Coding Scheme
Code Value
Code Meaning
HL7 v3 ActClass equivalent
SRT P
Specimen collection
SPECCOLLECT P
Specimen receiving
CONTREG
P3-4000A
Sampling of tissue specimen
PROC P
Staining
SPCTRT P
Specimen processing
DCM
111729
Specimen storage
STORE

39. Annotation and Segmentation

40. DICOM annotation principles
Annotations are conveyed in information objects separate from the original image Annotations may be created at a time much later than the image acquisition, and in a completely different environment Multiple annotation objects can reference the same image Selection of an annotation object for display implicitly invokes display of the referenced image

41. Annotation types
Presentation States Structured Reporting Segmentation

42. Presentation State
Softcopy Presentation States define how referenced image(s) will be displayed
Transforms to device independent grayscale/color space (LUTs)
Selection of display area (ROI) of the image
Image rotate or flip
Graphical and textual annotations, overlays, shutters
Grayscale, color, and pseudo-color SPSs
Blending SPS overlays a pseudo-color image on a grayscale image
E.g., for PET/CT
Blending on grayscale originals (currently no standard for blending of color originals)

43. Structured Reporting
Presentation State annotations are for human reading, not interoperable for automated applications
No controlled and coded vocabulary, no structural semantics (relationships between annotations)
SR important for (semi-)automated imaging analysis and review processes

44. Key Image Note
SR-type object that provides a classification and a textual comment for a referenced object
Formally known as “Key Object Selection”, but commonly denoted “Key Image Note” after IHE use case and profile
Classifications typically identify intended subsequent use of referenced objects
“For Referring Provider”, “For Research”, “For Report Attachment”
“Rejected for Quality Reasons”, “Signed Complete Study Content”

45. Segmentation Derived image object Multiple segments per object
Uses enhanced multi-frame mechanism
Multiple segments per object
Each segment linked to a categorization
Pixels show presence of category at pixel location
Binary (1-bit/pixel) or fractional (probability or occupancy)
Segmentation object is typically in same Frame of Reference as source image
Segments can be displayed as overlays on source image

46. Segmentation Example

47. Pathology in DICOM – Specimen and Workflow

48. What’s NOT in Sup145 All the modules already standardized
Patient, Study, Series, Equipment, General Image
Multi-Frame Functional Groups and Dimensions
Sup122 Specimen Module
Explicit description of workflow
Use of Modality Worklist, Modality Performed Procedure Step, Image Availability Notification, etc.

49. Sup 122 Specimen Identification
Support for pathology lab workflow, specimen-based imaging
Gross specimens, blocks, vials, slides
Image-guided biopsy samples
Specimen Module at image level of hierarchy
Identification, processing history
May be used with current Visible Light image object definitions
Update to Modality Worklist to convey Specimen Module
Enables automated slide scanning devices to fully populate header
Update to Modality Performed Procedure Step to identify imaged specimen
Allows LIS/APLIS to track images for specimens

50. Specimen Imaging Information Model
Basic DICOM Information Model
Disambiguates specimen and container
Container is target of image
Container may have more than one specimen
Specimens have a physical derivation (preparation) from parent specimens
When more than one specimen in an imaged container, each specimen is distinguished (e.g., by position or color-coding)

51. HL7 v3 ActClass equivalent
Preparation Step
0-n Preparation Steps per Specimen
Each Preparation Step described by 1-n structured Content Items (name:value pairs)
Acquisition Context plus structuring into steps
DICOM Template 8001 Specimen Preparation
Coding Scheme
Code Value
Code Meaning
HL7 v3 ActClass equivalent
SRT P
Specimen collection
SPECCOLLECT P
Specimen receiving
CONTREG
P3-4000A
Sampling of tissue specimen
PROC P
Staining
SPCTRT P
Specimen processing
DCM
111729
Specimen storage
STORE

52. Preparation steps example

53. Managed Workflow Concepts (IHE)
ORDER : A request for departmental service
REQUESTED PROCEDURE : Unit of work resulting in one Report with associated codified, billable acts
PROCEDURE STEP : The smallest unit of managed work in the workflow Scheduled Procedure Step: ‘A unit of work to do’ Performed Procedure Step: ‘A unit of work done’
Representation includes: healthcare providers, information systems vendors, imaging systems vendors, and standards groups participating

54. One Order – One Procedure – One Study – One Report
Simple Workflow
One Order – One Procedure – One Study – One Report
Imaging Department
DICOM Modality Worklist
ORDER
A request for Departmental Service
Scheduled Procedure
Step
Acquisition Modality
One or more series of images
Performed Procedure
Step
Set of Codifiable,
Billable, Acts
Requested
Procedure
Report
Representation includes: healthcare providers, information systems vendors, imaging systems vendors, and standards groups participating
Charles Parisot - IHE

55. Multiple Modality Steps
DICOM Modality Worklist
Imaging Department
ORDER
A request for Departmental Service
Scheduled Procedure
Step A
Acquisition Modality
One or more series of images
Performed Procedure
Step P1
Report
Set of Codifiable,
Billable, Acts
Requested
Procedure
DICOM Modality Worklist
Scheduled Procedure
Step B
Acquisition Modality
One or more series of images
Performed Procedure
Step P2
Representation includes: healthcare providers, information systems vendors, imaging systems vendors, and standards groups participating

56. Anatomic Pathology Imaging Workflow
Interpretation Worklist
by accession
Pathology order
Slide preparation
history data
LIS /
APLIS
Slide preparation
Imaging task
completion w/
list of images and specimen IDs
Specimen accessioning data
Modality Worklist Query
by slide barcode
Imaging task w/
slide preparation
history data
Workstation
Gross
specimen
accessioning
Images
Images
Whole Slide
Scanner
Surgical or
biopsy
procedure
Images w/ slide prep history
Images – X-ray, U/S, optical, etc.
PACS

57. Sup145 Whole Slide Imaging Proposal

58. Sup145 multi-frame tiling concept
Use multi-frame image objects (not object per tile)
Single frame image
Thumbnail Image
Multi-frame image
(single object)
Intermediate Image Tiles
Multi-frame image
(single object) may include multiple Z-planes, color planes
Baseline
Image Tiles
In 1 or more DICOM Series

59. Alternate approach (not in draft!)
Remove 64k2 image matrix restriction
Can leverage JPEG2000 Part2 multi-component compression Use JPEG Interactive Protocol capabilities
JPIP low-res view of baseline image
JPIP medium-res view of baseline image
Baseline
Image
Multi-frame (Z-planes, colors) image
(single object)

60. Total Pixel Matrix
Total Pixel Matrix Origin
Total pixel matrix origin at top left hand corner of imaged volume Frame (tile) rows and columns align with total pixel matrix rows and columns Frames limited to 216 columns and rows Total pixel matrix limited to 232 columns and rows
Columns →
Rows ↓
Frame Pixel Matrix Origin

61. Z-planes
Z-planes are identified as nominal physical height of image focal plane above reference surface (μm) Z-plane information is used for relative spatial positioning of image planes, and nominal inter-plane distance An image plane may track variable specimen thickness / surface contour, but only one Z-value used ↑ Z
Cover slip ↑ Z
Specimen
Slide substrate (glass)

62. Z planes track curved surface
Z plane 1, Z plane 2, Z plane 3, Z plane 4
Viktor Sebestyén Varga – 3DHISTECH Ltd.

63. Organization of tiles into objects
All valid:
Single Multi-frame image
Multi-frame image per Z-plane
Multi-frame image per spatial region

64. Sparse tiling
Multi-frame med-res image
Multi-frame hi-res image
Only selected tiles encoded Full image matrix might be encoded at lower resolution

65. Localizer Image Flavor
Thumbnail image (single frame) plus multi-resolution navigation links
Each tile of other resolution images has its corresponding area identified in thumbnail
Full description of target tiles
Object UID and frame #
Resolution
Z-plane
Multiple target frames can overlap
Different resolution, Z-plane, color, etc.
Presentation and any interactive behavior is not defined in standard

66. Label Image Flavor Purpose is to capture slide label
Any specimen captured is irrelevant
Image IOD includes Slide Label Module
Barcode (if deciphered)
Label Text (if deciphered)
Burned In Annotation (0028,0301) might be “NO” if the label includes only a specimen identifier and not patient identifying data

67. C Slide Coordinates
Used in VL Slide-Coordinates Microscopic Image IOD
Single frame image, typically from microscope-mounted camera
Used to localize center of VL SCM Image
DICOM Frame of Reference associated with slide corner origin
Reproducibility not guaranteed across different mountings of slide, even on same equipment
Label ↑ Y
Specimen
VL SCM Image area
X →
Slide Coordinates Origin
Cover slip ↑ Z
Specimen
Slide substrate (glass)

68. C.7.4.1 Frame Of Reference Module
When a Frame of Reference is identified, it is not important how the [imaging target] is positioned relative to the imaging equipment or where the origin of the Frame Of Reference is located. It is important that the position of the [imaging target] and the origin are constant in relationship to a specific Frame Of Reference The Position Reference Indicator may or may not coincide with the origin of the fixed frame of reference related to the Frame of Reference UID. The Position Reference Indicator shall be used only for annotation purposes and is not intended to be used as a mathematical spatial reference.

69. WSI Image Pixel Matrix ↓ ↑ ↑
Label
Columns →
Image Matrix not necessarily aligned to slide edge, nor to Slide-Coordinates Image Matrix origin (top left hand corner) located relative to Slide-Coordinates Frame of Reference origin (X,Y in mm) Direction of rows and columns given as cosines in Slide-Coordinates Frame of Reference Each tile (frame) TLHC located relative to Image Matrix origin (column, row) Each tile center located relative to Slide-Coordinates origin (X,Y in mm)
Rows ↓
X → ↑ Y
Image Matrix Origin
Slide-Coordinates Origin
Cover slip ↑ Z
Specimen
Slide substrate (glass)

70. Optical paths
Each combination of light source, lenses, illumination method, detected wavelengths, etc. used in an acquisition is an optical path
Each path described in an Item of the Optical Path Sequence
Examples:
Full spectrum light, transmission, RGB color sensors
uV light, excitation, blue monochrome sensor
Each frame may specify a different optical path
Allows different colors in a single object, including hyperspectral (n monochrome planes)
Identified in Optical Path Functional Group by reference to Optical Path Sequence Item

71. Optical paths What parameters are needed?
To be added in Part 16 Context Groups
Is a “macro image” simply a selected optical path?
Illumination:
Color(s)
Intensity
Type (laser)
Filters:
Color(s)
Polarization
Lens:
Illumination Method:
Transmission
Reflection
Scatter
Excitation
Lens:
Filters:
Color(s)
Polarization
Sensor:
Color(s)

72. WSI Functional Groups Standard WSI Specific
Pixel Measures (pixel spacing, layer thickness) – shared
Frame Content (datetime, dimensional location) – per-frame
Referenced Image, Derivation (if required for individual frames)
WSI Specific
Plane Position (relative to total matrix and to SCM FoR)
Optical Path
Specimen Reference (if multiple specimens on slide are automatically distinguishable)

73. Pixel Measures functional group
Attribute Name
Tag
Type
Attribute Description
Pixel Measures Sequence
(0028,9110) 1
Identifies the physical characteristics of the pixels of this frame. Only a single Item shall be permitted in this sequence.
>Pixel Spacing
(0028,0030) 1C
Physical distance in the imaging target (patient, specimen, or phantom) between the centers of each pixel, specified by a numeric pair - adjacent row spacing (delimiter) adjacent column spacing in mm. See for further explanation of the value order.
Note: In the case of CT images ...
Required if Volumetric Properties (0008,9206) is other than DISTORTED or SAMPLED. May be present otherwise.
>Slice Thickness
(0018,0050)
Nominal reconstructed slice thickness (for tomographic imaging) or depth of field (for optical imaging) in mm.
See C   and C for further explanation.
Required if Volumetric Properties (0008,9206) is VOLUME or SAMPLED. May be present otherwise.
Redefinition

74. Plane Position (Slide) functional group
Attribute Name
Tag
Type
Attribute Description
Plane Position (Slide) Sequence
(gggg,nn1A) 1
Describes position of frame in the Total Pixel Matrix and in the Slide Coordinate System Frame of Reference. Only a single Item may be present in this Sequence.
>Position In Image Pixel Matrix 
(gggg,nn1F)
The coordinate of the top left pixel of the frame in the Total Pixel Matrix (see C.8.12.X3.1.1), given as column\row. Column is the horizontal position and row is the vertical position. The coordinate of the top left pixel of the Total Pixel Matrix is 1\1.
>Image Center Point Coordinates Sequence 
(0040,071A)
Identifies the coordinates of the center point of this frame in the Slide Coordinate System Frame of Reference. Only a single Item shall be permitted in this sequence. See Section C for further explanation.
Note: This attribute allows simplified transformation of a single frame of a multi-frame VL WSI SOP Instance into an instance of the VL Slide Coordinates Microscopy SOP Class.
>>X Offset in Slide Coordinate System
(0040,072A)
The X offset in millimeters from the Origin of the Slide Coordinate System. See Figure C.8-16.
>>Y Offset in Slide Coordinate System
(0040,073A)
The Y offset in millimeters from the Origin of the Slide Coordinate System. See Figure C.8-16.
>Z Offset in Slide Coordinate System
(0040,074A)
The Z offset in microns from the Origin of the Slide Coordinate System, nominally the surface of the glass slide substrate. See Figure C.8-17
Note: Required even if only a single focal plane was acquired.
Do we need to separate to two attributes to support independent dimensions?
Do we really need this sequence introducer (consistency w/ C )? Could just specify X and Y as center point coordinates

75. Dimensions
Based on attributes in functional groups (i.e., values that change on a per-frame basis)
Typical dimensions for WSI:
Total Matrix Column Origin
Total Matrix Row Origin
Z-Plane
Optical Path (color/polarization)
Attributes used for Dimensions specified in Multi-frame Dimension Module
Each frame specifies its dimensional indexes in Frame Content functional group
Index values (ordinals) mapped to dimensional attribute values
E.g., with (Column, Row) dimensions, and pixel frames, frame with index value (2,3) would have origin column\row values of 8193\12289

76. Annotations of WSI - Segmentations
Segmentations can be created frame-by-frame / pixel-by-pixel against selected frames of original image
Reference through Derivation Image Functional Group
1-bit/source-pixel, or 8-bits/source-pixel
Segmentations can be created against arbitrary areas within a specified Frame of Reference
Requires Plane Position and Plane Orientation Functional Groups – may not be usable with slide coordinates Frame of Reference
Display of segmentation can implicitly invoke a non-standardized overlay or blending with source image
Segmentation can specify its preferred color

77. Annotations of WSI - Presentation States
Color Presentation State supports annotation of a source image
Displayed Area Selection allows up to rows/columns, currently relative to frame-based rows/columns
Proposed enhancement (with new attribute and new enumerated value) to allow Displayed Area Selection and annotation location relative to WSI total matrix, rather than to frame
Implicitly applies to all dimensions (Z-planes, colors), only constrained by explicit frame numbers; should there be a general mechanism to limit by dimension (as is done for segments)?
Placement of annotations limited to 24-bit precision (IEEE bit float)
May be image relative or selected display area relative
Allows sub-pixel resolution up to 8M rows/columns for image relative

78. Presentation State - Displayed Area Selection
Attribute Name
Tag
Type
Attribute Description
Displayed Area Selection Sequence
(0070,005A) 1
A sequence of Items each of which describes the displayed area selection for a group of images or frames. Sufficient Items shall be present to describe every image and frame listed in the Presentation State Relationship Module.
One or more Items shall be present.
>Referenced Image Sequence
(0008,1140) 1C
>>Include ‘Image SOP Instance Reference Macro’ Table 10-3
>Pixel Origin Interpretation
(gggg,bb01)
For a referenced multi-frame image, specifies whether the Displayed Area Top Left Hand Corner (0070,0052)
and Displayed Area Bottom RIght Hand Corner (0070,0053) are to be interpreted relative to the individual frame pixel origins, or relative to the Total Pixel Matrix origin (see C.8.12.X3.1.1).
Required if the Referenced Image Sequence (0008,1140) >Referenced SOP Class UID (0008,1150) value is xxx (VL Whole Slide Microscopy Image). May be present otherwise.
Enumerated Values:
FRAME
VOLUME
If not present, TLHC and BRHC are defined relative to the frame pixel origins.
>Displayed Area Top Left Hand Corner
(0070,0052)
>Displayed Area Bottom Right Hand Corner
(0070,0053) …

79. Presentation State - Graphic Annotation Units
Attribute Name
Tag
Type
Attribute Description
Graphic Annotation Sequence
(0070,0001) 1
A sequence of Items each of which represents a group of annotations composed of graphics or text or both.
One or more Items shall be present. …
>>Bounding Box Annotation Units
(0070,0003) 1C
Units of measure for the axes of the text bounding box.
Defines whether or not the annotation is Image or Displayed Area relative. Both dimensions shall have the same units.
Enumerated Values:
PIXEL = Image relative position specified with sub-pixel resolution such that the origin at the Top Left Hand Corner (TLHC) of the TLHC pixel is 0.0\0.0, the Bottom Right Hand Corner (BRHC) of the TLHC pixel is 1.0\1.0, and the BRHC of the BRHC pixel is Columns\Rows (see figure C ). The values must be within the range 0\0 to Columns\Rows.
DISPLAY = Fraction of Specified Displayed Area where 0.0\0.0 is the TLHC and 1.0\1.0 is the BRHC. The values must be within the range 0.0 to 1.0.
MATRIX = Image relative position specified with sub-pixel resolution such that the origin at the Top Left Hand Corner (TLHC) of the TLHC pixel of the Total Pixel Matrix is 0.0\0.0, the Bottom Right Hand Corner (BRHC) of the TLHC pixel is 1.0\1.0, and the BRHC of the BRHC pixel of the Total Pixel Matrix is Total Pixel Matrix Columns\Total Pixel Matrix Rows (see C.8.12.X3.1.3). The values must be within the range 0\0 to Total Pixel Matrix Columns\Total Pixel Matrix Rows. This value is valid only if the Referenced Image Sequence (0008,1140) >Referenced SOP Class UID (0008,1150) value is xxx (VL Whole Slide Microscopy Image).
Required if Bounding Box Top Left Hand Corner (0070,0010) or Bounding Box Bottom Right Hand Corner (0070,0011) is present.

80. Modality Worklist Scheduled Specimen Sequence added to MWL in Sup122
Allows query by Container ID (slide barcode)
Allows return from SCP of complete Specimen Module (slide processing history to be used for imaging set up and/or inclusion in WSI header
Other parameters can be passed in Protocol Context Sequence
Template specification for Content Items
Proposed Protocol Optical Paths Sequence
Parallel to Protocol Context Sequence
General VL attributes