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  Indian J Med Microbiol
 

Figure 3: Encoding of specimen information in DICOM data set. (a) DICOM model of the real world for pathology laboratory workflow. Top: Hierarchical relationships between the patient (blue), study =case (purple), specimen (yellow), and container (green) information entities. Bottom: Sequence of specimen preparation steps (1-6) for a typical surgical pathology encounter. (b) DICOM data set of image instance with encoded laboratory information. Patient and Study entities are described by attributes of the Patient module (blue) and general study and patient study modules (purple), respectively. Specimen and container entities are described by attributes of the Specimen module (yellow). The container used for imaging (glass slide) is described at the root dataset level whereas imaged specimens (tissue sections) are described by the nested specimen description sequence attribute. Laboratory procedures that were performed to prepare a specimen for image acquisition are described by the specimen preparation sequence attribute, which includes a specimen preparation step content item sequence attribute for each performed procedure. The description of a content item is based on the Specimen Preparation template, which provides concepts to encode a procedure as name-value pairs using a specified coding scheme, such as SNOMED CT. Mandatory concepts are the specimen identifier, which describes the identifier of the processed specimen, and processing type, which describes the kind of procedure that was performed. Additional concepts may be included depending on the value of the Processing Type concept. In case of a sampling preparation step (highlighted in red , compare sequence step 3 in a), Sampling method, Parent Specimen Identifier and Parent Specimen Type concepts are included. (c) Schematic of a current pathology report. Top: Identifiable information about patient (blue) and accession (purple), which map to attributes of the patient and general study module. Bottom: Final diagnosis and gross description for each specimen of type “part.” Identifiable information about specimen of type “section” is often not included in the report (i.e., final diagnoses generally lack complete slide-level annotations). SNOMED CT: Systematized Nomenclature of Medicine Clinical Terms

Figure 3: Encoding of specimen information in DICOM data set. (a) DICOM model of the real world for pathology laboratory workflow. Top: Hierarchical relationships between the patient (blue), study =case (purple), specimen (yellow), and container (green) information entities. Bottom: Sequence of specimen preparation steps (1-6) for a typical surgical pathology encounter. (b) DICOM data set of image instance with encoded laboratory information. Patient and Study entities are described by attributes of the Patient module (blue) and general study and patient study modules (purple), respectively. Specimen and container entities are described by attributes of the Specimen module (yellow). The container used for imaging (glass slide) is described at the root dataset level whereas imaged specimens (tissue sections) are described by the nested specimen description sequence attribute. Laboratory procedures that were performed to prepare a specimen for image acquisition are described by the specimen preparation sequence attribute, which includes a specimen preparation step content item sequence attribute for each performed procedure. The description of a content item is based on the Specimen Preparation template, which provides concepts to encode a procedure as name-value pairs using a specified coding scheme, such as SNOMED CT. Mandatory concepts are the specimen identifier, which describes the identifier of the processed specimen, and processing type, which describes the kind of procedure that was performed. Additional concepts may be included depending on the value of the Processing Type concept. In case of a sampling preparation step (highlighted in red , compare sequence step 3 in a), Sampling method, Parent Specimen Identifier and Parent Specimen Type concepts are included. (c) Schematic of a current pathology report. Top: Identifiable information about patient (blue) and accession (purple), which map to attributes of the patient and general study module. Bottom: Final diagnosis and gross description for each specimen of type “part.” Identifiable information about specimen of type “section” is often not included in the report (i.e., final diagnoses generally lack complete slide-level annotations). SNOMED CT: Systematized Nomenclature of Medicine Clinical Terms