Computed Radiography ImageCIOD
CT ImageCIOD
MR ImageCIOD
Nuclear Medicine ImageCIOD
Ultrasound ImageCIOD
Ultrasound Multi-frame ImageCIOD
Secondary Capture ImageCIOD
Multi-frame Single Bit Secondary Capture ImageCIOD
Multi-frame Grayscale Byte Secondary Capture ImageCIOD
Multi-frame Grayscale Word Secondary Capture ImageCIOD
Multi-frame True Color Secondary Capture ImageCIOD
X-Ray Angiographic ImageCIOD
X-Ray Radiofluoroscopic ImageCIOD
RT ImageCIOD
RT DoseCIOD
RT Structure SetCIOD
RT PlanCIOD
Positron Emission Tomography ImageCIOD
Digital X-Ray ImageCIOD
Digital Mammography X-Ray ImageCIOD
Digital Intra-Oral X-Ray ImageCIOD
RT Beams Treatment RecordCIOD
RT Brachy Treatment RecordCIOD
RT Treatment Summary RecordCIOD
VL Endoscopic ImageCIOD
VL Microscopic ImageCIOD
VL Slide-Coordinates Microscopic ImageCIOD
VL Photographic ImageCIOD
Video Endoscopic ImageCIOD
Video Microscopic ImageCIOD
Video Photographic ImageCIOD
VL Whole Slide Microscopy ImageCIOD
PatientMModule - Patient
Clinical Trial SubjectUModule - Patient
General StudyMModule - Study
Patient StudyUModule - Study
Clinical Trial StudyUModule - Study
General SeriesMModule - Series
Whole Slide Microscopy SeriesMModule - Series
Clinical Trial SeriesUModule - Series
Frame of ReferenceMModule - Frame of Reference
General EquipmentMModule - Equipment
Enhanced General EquipmentMModule - Equipment
General AcquisitionMModule - Acquisition
Multi-Resolution PyramidUModule - Multi-Resolution Pyramid
General ImageMModule - Image
General ReferenceUModule - Image
Microscope Slide Layer Tile OrganizationMModule - Image
(0048,0006) Total Pixel Matrix Columns1Unsigned Long
(0048,0007) Total Pixel Matrix Rows1Unsigned Long
(0048,0008) Total Pixel Matrix Origin Sequence1Sequence
(0040,072A) X Offset in Slide Coordinate System1Decimal String
(0040,073A) Y Offset in Slide Coordinate System1Decimal String
(0040,074A) Z Offset in Slide Coordinate System1CDecimal String
(0048,0102) Image Orientation (Slide)1CDecimal String
(0048,0303) Total Pixel Matrix Focal Planes1CUnsigned Long
Image PixelMModule - Image
Acquisition ContextMModule - Image
Multi-frame Functional GroupsMModule - Image
Multi-frame DimensionMModule - Image
SpecimenMModule - Image
Whole Slide Microscopy ImageMModule - Image
Optical PathMModule - Image
Slide LabelCModule - Image
SOP CommonMModule - Image
Common Instance ReferenceMModule - Image
Frame ExtractionCModule - Image
Real-Time Video Endoscopic ImageCIOD
Real-Time Video Photographic ImageCIOD
Dermoscopic Photography ImageCIOD
Grayscale Softcopy Presentation StateCIOD
Color Softcopy Presentation StateCIOD
Pseudo-Color Softcopy Presentation StateCIOD
Blending Softcopy Presentation StateCIOD
Basic Structured DisplayCIOD
XA/XRF Grayscale Softcopy Presentation StateCIOD
Advanced Blending Presentation StateCIOD
Variable Modality LUT Softcopy Presentation StateCIOD
Basic Voice Audio WaveformCIOD
12-Lead ECGCIOD
General ECGCIOD
Ambulatory ECGCIOD
Hemodynamic WaveformCIOD
Basic Cardiac Electrophysiology WaveformCIOD
Arterial Pulse WaveformCIOD
Respiratory WaveformCIOD
General Audio WaveformCIOD
Real-Time Audio WaveformCIOD
Routine Scalp ElectroencephalogramCIOD
ElectromyogramCIOD
ElectrooculogramCIOD
Sleep ElectroencephalogramCIOD
Multi-channel Respiratory WaveformCIOD
Body Position WaveformCIOD
General 32-bit ECGCIOD
Basic Text SRCIOD
Enhanced SRCIOD
Comprehensive SRCIOD
Key Object Selection DocumentCIOD
Mammography CAD SRCIOD
Chest CAD SRCIOD
Procedure LogCIOD
X-Ray Radiation Dose SRCIOD
Spectacle Prescription ReportCIOD
Colon CAD SRCIOD
Macular Grid Thickness and Volume ReportCIOD
Implantation Plan SR DocumentCIOD
Comprehensive 3D SRCIOD
Radiopharmaceutical Radiation Dose SRCIOD
Extensible SRCIOD
Acquisition Context SRCIOD
Simplified Adult Echo SRCIOD
Patient Radiation Dose SRCIOD
Planned Imaging Agent Administration SRCIOD
Performed Imaging Agent Administration SRCIOD
Rendition Selection DocumentCIOD
Enhanced X-Ray Radiation Dose SRCIOD
Enhanced MR ImageCIOD
MR SpectroscopyCIOD
Enhanced MR Color ImageCIOD
Raw DataCIOD
Enhanced CT ImageCIOD
Spatial RegistrationCIOD
Deformable Spatial RegistrationCIOD
Spatial FiducialsCIOD
Ophthalmic Photography 8 Bit ImageCIOD
Ophthalmic Photography 16 Bit ImageCIOD
Stereometric RelationshipCIOD
Hanging ProtocolCIOD
Encapsulated PDFCIOD
Encapsulated CDACIOD
Real World Value MappingCIOD
Enhanced XA ImageCIOD
Enhanced XRF ImageCIOD
RT Ion PlanCIOD
RT Ion Beams Treatment RecordCIOD
SegmentationCIOD
Ophthalmic Tomography ImageCIOD
X-Ray 3D Angiographic ImageCIOD
X-Ray 3D Craniofacial ImageCIOD
Breast Tomosynthesis ImageCIOD
Enhanced PET ImageCIOD
Surface SegmentationCIOD
Color PaletteCIOD
Enhanced US VolumeCIOD
Lensometry MeasurementsCIOD
Autorefraction MeasurementsCIOD
Keratometry MeasurementsCIOD
Subjective Refraction MeasurementsCIOD
Visual Acuity MeasurementsCIOD
Ophthalmic Axial MeasurementsCIOD
Intraocular Lens CalculationsCIOD
Generic Implant TemplateCIOD
Implant Assembly TemplateCIOD
Implant Template GroupCIOD
RT Beams Delivery InstructionCIOD
Ophthalmic Visual Field Static Perimetry MeasurementsCIOD
Intravascular Optical Coherence Tomography ImageCIOD
Ophthalmic Thickness MapCIOD
Surface Scan MeshCIOD
Surface Scan Point CloudCIOD
Legacy Converted Enhanced CT ImageCIOD
Legacy Converted Enhanced MR ImageCIOD
Legacy Converted Enhanced PET ImageCIOD
Corneal Topography MapCIOD
Breast Projection X-Ray ImageCIOD
Parametric MapCIOD
Wide Field Ophthalmic Photography Stereographic Projection ImageCIOD
Wide Field Ophthalmic Photography 3D Coordinates ImageCIOD
Tractography ResultsCIOD
RT Brachy Application Setup Delivery InstructionCIOD
Planar MPR Volumetric Presentation StateCIOD
Volume Rendering Volumetric Presentation StateCIOD
Content Assessment ResultsCIOD
CT Performed Procedure ProtocolCIOD
CT Defined Procedure ProtocolCIOD
Protocol ApprovalCIOD
XA Performed Procedure ProtocolCIOD
XA Defined Procedure ProtocolCIOD
Ophthalmic Optical Coherence Tomography En Face ImageCIOD
Ophthalmic Optical Coherence Tomography B-scan Volume AnalysisCIOD
Encapsulated STLCIOD
Encapsulated OBJCIOD
Encapsulated MTLCIOD
RT Physician IntentCIOD
RT Segment AnnotationCIOD
RT Radiation SetCIOD
C-Arm Photon-Electron RadiationCIOD
Tomotherapeutic RadiationCIOD
Robotic-Arm RadiationCIOD
RT Radiation Record SetCIOD
RT Radiation Salvage RecordCIOD
C-Arm Photon-Electron Radiation RecordCIOD
Tomotherapeutic Radiation RecordCIOD
Robotic-Arm Radiation RecordCIOD
RT Radiation Set Delivery InstructionCIOD
RT Treatment PreparationCIOD
Enhanced RT ImageCIOD
Enhanced Continuous RT ImageCIOD
RT Patient Position Acquisition InstructionCIOD
Microscopy Bulk Simple AnnotationsCIOD
InventoryCIOD
Photoacoustic ImageCIOD
Confocal Microscopy ImageCIOD
Confocal Microscopy Tiled Pyramidal ImageCIOD
Basic DirectoryCIOD

Built with by Innolitics, a team of medical imaging software developers.

Data synced with official DICOM standard on 19 March 2024. The DICOM Standard is under continuous maintenance, and the current official version is available at http://www.dicomstandard.org/current/. DICOM Parts 3, 4, and 6, © NEMA. Please note that the most recent PDF version of the standard is the official reference, and should checked when making technical decisions.

Total Pixel Matrix Origin Sequence Attribute

Tag(0048,0008)
TypeRequired (1)
KeywordTotalPixelMatrixOriginSequence
Value Multiplicity1
Value RepresentationSequence (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

  1. The Label of the Slide is presumed to be mounted-on or written-on the Top Surface of the Slide.

  2. 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

  1. 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.

  2. 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.

  3. 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.

  4. 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.

Figure C.8-17b. In-vivo microscopy coordinates a) is a front on view b) is top-down view of in-vivo imaging