supplement 145 whole slide imaging – background and design decisions harry solomonge healthcare

Supplement 145 Whole Slide Imaging –background and design decisions

Harry Solomon GE Healthcare

2 Sup 145 WSIHarry Solomon

DICOM BASICS


DICOM Image Information Object Definition

PatientModule

PatientStudy

Module

GeneralSeriesModule

GeneralStudy

Module

Frame ofReference

Module

GeneralEquipment

Module

GeneralImage

Module

ImagePlane

Module

Contrast/Bolus

Module

ImagePixel

Module

ModalityImage

Module

Multi-frame

Module…

VOILUT

Module

SOPCommonModule

PatientInformation

StudyInformation

SeriesInformation

Image(Instance)

Information

Patient NamePatient ID

Patient SexPatient Birthdate

Study Unique IDAccession Number

Study Date/TimeStudy Description

Referring MD

Rows/ColumnsBits per PixelPhotometric

DICOM CompositeInformation Model

Hierarchy

Dwight Simon


Data Element Encoding

0020000Dhex UI 1.2.840.1.113709.9.0.0.5743.14575602.126hex

Study InstanceUnique Identifier

(0020,000D)

Instance UID encoded as “dotted decimal”

Data Set

Data Element

Tag Value Length Value Field

optional field - dependent on negotiated Transfer Syntax

ValueRepresen-

tation

Data Elem. Data Elem.Data Elem. Data Elem.

order of transmission

Attributes are the logical concepts associated with an information entity

Data elements are how attributes are encoded in an information object

Similar to TIFF


(0008,0005) CS 30 ISO 2022 IR 13\ISO 2022 IR 87

(0008,0008) CS 22 ORIGINAL\PRIMARY\AXIAL

(0008,0016) UI 26 1.2.840.10008.5.1.4.1.1.2

(0008,0018) UI 58 1.2.392.200036.9116.2.6.1.48.1211393615.1211874194.564494

(0008,0020) DA 8 20080527

(0008,0021) DA 8 20080527

(0008,0022) DA 8 20080527

(0008,0023) DA 8 20080527

(0008,0030) TM 10 163836.000

(0008,0031) TM 10 164306.390

(0008,0032) TM 10 164039.850

(0008,0033) TM 10 164040.397

(0008,0050) SH 8 5162581

(0008,0060) CS 2 CT

(0008,0070) LO 8 TOSHIBA

…

(7FE0,0010) OW 524288 00 00 00 00 ff ff ff ff 00 0f 4c 4a 49 46 00 01...

Part of a DICOM object

Tags in increasing numeric orderValue length always an even numberAttributes related to modules and

information model levels all jumbled up

PatientInformation

StudyInformation

SeriesInformation

Image(Instance)

Information


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


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


Example: Scheduled Protocol Code Sequence attribute


Scheduled Protocol Code Sequence attributeScheduled Protocol Code Sequence (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 (0008,0100)

>>>Coding Scheme Designator (0008,0102)

>>>Coding Scheme Version (0008,0103)

>>>Code Meaning (0008,0104)

>>DateTime (0040,A120)

>>Person Name (0040,A123)

>>Text Value (0040,A160)

>>Concept Code Sequence (0040,A168)

>>>Code Value (0008,0100)

…

>>Content Item Modifier Sequence (0040,0441)

>>>Value Type (0040,A040)

>>>Concept Name Code Sequence (0040,A043)

>>>>Code Value (0008,0100)

>>>>Coding Scheme Designator (0008,0102)

…

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

Sequence Data Element


ValueRepresen-tation SQ

ItemIntroducer

Attribute1

Attribute2

ItemDelimiter

ItemIntroducer

Attribute1

Attribute2

ItemDelimiter

SequenceDelimiter

May be “undefined length”

Specifies length of Item, or may say “undefined length”

Required if “undefined length” Item

Required if “undefined length” Sequence Attribute


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

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)

Pixel Data Element


ValueRepresen-tation OB

ItemIntroducer

Basic OffsetTable

SequenceDelimiter

May be “undefined length

Specifies length of Basic Offset Table

Required if “undefined length” Pixel Data Attribute

(7FE0,0010)

ItemIntroducer

Encapsulated StreamFragment 1

ItemIntroducer

Encapsulated StreamFragment 2

Specifies length of Stream Fragment


MULTIFRAME IMAGES


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 1000+ image studies• Dynamic image header supports functional or acquisition

attributes changing during scan• Dimensions allow multiple views of data

File size flexibility through concatenations


Single-frame to MultiFrame

N Objects, N Headers

N Frames, One Header

Pixel dataDimension dataPer-frame headerFixed Header


Functional Groups and the Per-Frame Header

Other attributes

Per-frame Functional Groups Sequence

Shared Functional Groups Sequence

> Functional Group A

> Functional Group B

> Functional Group M

…..

Other attributes

Functional Groups with attributes constant for all

frames

Item 1 (Frame 1) Sequence of

Functional Groups for each individual frame

Pixel Data

Frame 1

Frame 2

Frame n

…..

> Functional Group C



…..

Item n (Frame n)




Item 2 (Frame 2)


…..

…..

…..

…..

> Functional Group K


Table C.7.6.16-8 CARDIAC SYNCHRONIZATION MACRO ATTRIBUTES

Attribute Name Tag Type Attribute Description

Cardiac Synchronization Sequence (0018,9118) 1

>Nominal Percentage of Cardiac Phase (0020,9241) 1C

>Nominal Cardiac Trigger Delay Time (0020,9153) 1

>Actual Cardiac Trigger Delay Time (0020,9252) 1C

>Intervals Acquired (0018,1083) 3

>Intervals Rejected (0018,1084) 3

>Heart Rate (0018,1088) 3

>R – R Interval Time Nominal (0020,9251) 1C

>Low R-R Value (0018,1081) 3

>High R-R Value (0018,1082) 3

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


position

time

b-value

cardiac phase

volume

orientation

time

echo

Dimensions – properties that may change


Phase (Time) Position Index

65

43

21

65

43

21

1 2 3

65

43

21

Physical Location(Stack) Index

Frame number 1-6 Frame number 7-12Frame number 13-18

Slice Order for phase 1

Phase order for slice 2

Image frames can be sorted/displayed independent of encoded frame order

Multi-phase / Multi-slice


Concatenations

What is a concatenation?• 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


An object may be split up into two or more SOP Instances, using the same concatenation UID

Legend:

Pixel data (not on scale)

Dimension data (not on scale)

Per-frame header

Fixed Header

Concatenations


IMAGE RETRIEVAL


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

Retrieve Request

Image(s) Send

Store Response(s)

Retrieve Response

Query Match(es)PACS

Query/RetrieveSCP

Query/RetrieveSCU

Workstation


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


Typical Hierarchical Query

PACS

Query/RetrieveSCP

Query/RetrieveSCU

WorkstationLevel: STUDYPatient ID: D73001Date: 20090521-20090524

Study ID: 09-35541Study UID: 1.2.789.45.63Patient ID: D73001Date: 20090521



Level: SERIESStudy UID: 1.2.789.87.11

Study UID: 1.2.789.87.11Series Num: 2Series UID: 1.2.405.31.2Modality: CT

Study UID: 1.2.789.87.11Series Num: 1Series UID: 1.2.405.31.1Modality: CT

Level: IMAGEStudy UID: 1.2.789.87.11Series UID: 1.2.405.31.1

Study UID: 1.2.789.87.11Series UID: 1.2.405.31.1Image UID: 1.2.405.31.1.99.1




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 1.2.789.87.11• Retrieve all objects under Study UID 1.2.789.87.11 / Series UID

1.2.405.31.1• Retrieve single object Study UID 1.2.789.87.11 / Series UID

1.2.405.31.1 / Instance UID 1.2.405.31.1.99.1

Retrieved objects sent and confirmed as wholes


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)


Frame-based retrieve

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

New in

2009

Supplement

119


VOCABULARY AND STRUCTURED REPORTING


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?


Name-value pairs

< BodyPartExamined “ABDOMENPELVIS” />

<el> <name “BodyPartExamined” /><value “ABDOMENPELVIS” />

</el>

<el><name code=00180015 system=DICOM meaning=“Body

Part Examined” /> <value code=R-FAB57 system=SNOMED

meaning=“Abdomen and pelvis” /></el>

00180015 = Body Part Examined

00180015 ABDOMENPELVIS

Why would we want to do this?


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


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)


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

Code SequencesTable 8.8-1 Common Attribute Set for Code Sequence Attributes

(Invoked as “Code Sequence Macro”) Attribute Name Tag Type Attribute Description

Code Value (0008,0100) 1 See Section 8.1.

Coding Scheme Designator

(0008,0102) 1 See Section 8.2.

Coding Scheme Version

(0008,0103) 1C See Section 8.2. Required if the value of Coding Scheme Designator (0008,0102) is not sufficient to identify the Code Value (0008,0100) unambiguously.

Code Meaning (0008,0104) 1 See Section 8.3.

DICOMPart 3

“Triplet coding” : code value, scheme, meaning(version seldom used)

Context Groups (Value Sets)

DICOMPart 3

DICOMPart 16

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)

Content Item

Concept NameSequence

(0040,A043)

Value Type

(0040,A040)

DateTime Value (0040,A120)

Text Value (0040,A160)

Code(0008,0100)

Scheme(0008,0102)

Meaning(0008,0104)

Concept ValueSequence

(0040,A168)

Code(0008,0100)

Scheme(0008,0102)

Meaning(0008,0104)

Person Name Value (0040,A123)

Referenced SOP Sequence

(0008,1199)

Numeric Value

(0040,A30A)

Measurement Units Sequence

(0040,08EA)

Code(0008,0100)

Scheme(0008,0102)

Meaning(0008,0104)

SOP Class UID(0008,0050)

SOP Instance UID(0008,0055)

UID Value (0040,A124)

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 P3-02000 Specimen collection SPECCOLLECT

SRT P3-05013 Specimen receiving CONTREG

SRT P3-4000A Sampling of tissue specimen PROC

SRT P3-00003 Staining SPCTRT

SRT P3-05000 Specimen processing SPCTRT

DCM 111729 Specimen storage STORE


ANNOTATION AND SEGMENTATION


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


Annotation types

Presentation States

Structured Reporting

Segmentation


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)


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


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”


Segmentation

Derived image 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


Segmentation Example

Segment Sequence

Other attributes

Item 1 (Segment 1)

Pixel Data

Frame 1

Frame 2

Frame 4

Item 2 (Segment 2)

Segment Number = 1

Segment Name = White Matter

Segment Category = Brain

Segment Type = White Matter

Segment Number = 2

Segment Name = Grey Matter


Segment Type = Grey Matter

Per-frame Functional Groups Sequence

Item 1 (Frame 1)

Segment Identification Sequence

Referenced Segment Number = 2


Item 1

Item 2 (Frame 2)



Item 1

Item 3 (Frame 3)

Frame 3

Shared Functional Groups Sequence

Item 1 (Shared – all frames)

Derivation Image Sequence

Item 3 (Segment 3)

Segment Number = 3

Segment Name = Lesion Part 1


Segment Type = Lesion

Item 4 (Segment 4) Segment Number = 4

Segment Name = Lesion Part 2


Segment Type = Lesion



Item 1

Item 4 (Frame 4)


Item 1

Item 1

Reference to source image (external object)

White Matter Gray Matter, CSFand Partial Volume

Lesion – Part 1 Lesion – Part 2

Binary Segmentation Results

Segment 12

3 4

Segment 2

Segment 3Segment 4


PATHOLOGY IN DICOM – SPECIMEN AND WORKFLOW


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.


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


SpecimenPhysical object

ContainerBox, Block, Slide, etc.

Is child of

n

PreparationStep

Collect, Sample, Stain, Process

Image

Isacquired

on

1

Series

1

Contains

n

1

CreatesEquipment

Modality

1 n

Study

Contains

Patient

1

Has

n

1

n

Issource

of

1

Contains

Contains1 n

n

Has1 n

1

Has

1ComponentBase, Coverslip

n

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)

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 P3-02000 Specimen collection SPECCOLLECT

SRT P3-05013 Specimen receiving CONTREG

SRT P3-4000A Sampling of tissue specimen PROC

SRT P3-00003 Staining SPCTRT

SRT P3-05000 Specimen processing SPCTRT

DCM 111729 Specimen storage STORE

Preparation steps example


Managed Workflow Concepts (IHE)

PROCEDURE STEP : The smallest unit of managed workin the workflow

Scheduled Procedure Step: ‘A unit of work to do’Performed Procedure Step: ‘A unit of work done’

ORDER : A request for departmental

service

REQUESTED PROCEDURE : Unit of work resulting in one Report

with associated codified, billable acts


Simple Workflow

One Order – One Procedure – One Study – One Report

AcquisitionModality

ORDERA request for DepartmentalService

Imaging Department

Set of Codifiable,

Billable, ActsOne or more series of images

PerformedProcedure

StepRequestedProcedure

ScheduledProcedure

Step

Report

DICOMModality Worklist

Charles Parisot - IHE

AcquisitionModality

AcquisitionModality

Multiple Modality Steps

ORDERA request for DepartmentalService

Imaging Department

Set of Codifiable,

Billable, ActsOne or more series of images

PerformedProcedure

Step P1

ScheduledProcedure

Step B

RequestedProcedure

ScheduledProcedure

Step A

Report

One or more series of images

PerformedProcedure

Step P2




Anatomic Pathology Imaging Workflow

Slide preparationSlide preparation history data

Whole Slide Scanner

Modality Worklist Queryby slide barcode

Images w/slide prep history

Imaging task completion w/list of imagesand specimen IDs

Workstation

Images

Interpretation Worklistby accession

Gross specimen

accessioning

Images

Surgical or biopsy

procedure

Images – X-ray, U/S, optical, etc.

Specimen accessioning data

Imaging task w/slide preparation history data

Pathology order


SUP145 WHOLE SLIDE IMAGING PROPOSAL


Sup145 multi-frame tiling concept

In 1 or more DICOM Series

Thumbnail Image

Intermediate Image Tiles

BaselineImage Tiles

Multi-frame image(single object)

Multi-frame image(single object)may include multipleZ-planes, color planes

Single frame image

Use multi-frame image objects (not object per tile)


Alternate approach (not in draft!)

BaselineImage

JPIP low-res view of baseline image

Multi-frame (Z-planes, colors) image(single object)

Remove 64k2 image matrix restrictionCan leverage JPEG2000 Part2 multi-component compressionUse JPEG Interactive Protocol capabilities

JPIP medium-res view of baseline image


Total Pixel Matrix

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

Total Pixel Matrix Origin

Columns →Rows

↓

Frame Pixel Matrix Origin


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 usedSpecimen↑

Z

Cover slip

↑Z

Slide substrate (glass)


Z planes track curved surface

Z plane 1, Z plane 2, Z plane 3, Z plane 4

Viktor Sebestyén Varga – 3DHISTECH Ltd.


Organization of tiles into objects

All valid:

Single Multi-frame image

Multi-frame image per Z-plane

Multi-frame image per spatial region


Sparse tiling

Only selected tiles encoded

Full image matrix might be encoded at lower resolution

Multi-frame hi-res image

Multi-frame med-res image


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


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

Labe

l


C.8.12.2 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

X →

↑Y

Specimen

Specimen

Slide Coordinates Origin

↑Z

Cover slip


VL SCM Image area


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.


WSI Image Pixel Matrix

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)

Columns →Rows

↓

Specimen

Labe

l

Slide-Coordinates Origin

↑Z

Cover slip


X →

↑ Y

Image Matrix Origin


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


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)IntensityType (laser)

Filters:Color(s)Polarization

Lens: Illumination Method:TransmissionReflectionScatterExcitation

Lens: Filters:Color(s)Polarization

Sensor:Color(s)


WSI Functional Groups

Standard• 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)


Pixel Measures functional group

Redefinition


Plane Position (Slide) functional group

Attribute Name Tag Type Attribute DescriptionPlane 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) 1 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) 1 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.8.12.2.1.1 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) 1 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) 1 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) 1 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 really need this sequence introducer (consistency w/ C.8.12.2)? Could just specify X and Y as center point coordinates

Do we need to separate to two attributes to support independent dimensions?


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 40962 pixel frames, frame with index

value (2,3) would have origin column\row values of 8193\12289


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


Annotations of WSI - Presentation States

Color Presentation State supports annotation of a source image

Displayed Area Selection allows up to 231-1 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 754 32-bit float)• May be image relative or selected display area relative• Allows sub-pixel resolution up to 8M rows/columns for image relative


Presentation State - Displayed Area Selection

Attribute Name Tag Type Attribute DescriptionDisplayed 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) 1C 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 1.2.840.10008.5.1.4.1.1.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) 1

>Displayed Area Bottom Right Hand Corner

(0070,0053) 1

…


Presentation State - Graphic Annotation Units

Attribute Name Tag Type Attribute DescriptionGraphic 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.10.5-1). 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 1.2.840.10008.5.1.4.1.1.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.


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

supplement 145 whole slide imaging – background and design decisions harry solomonge healthcare

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