SpecimenTable.md

4.4.2. Specimen_Table

The specimen table is used to intialize the slides into the pipeline. This table also serves as the link between the names on the slides, the Specimen #s, and the de-identified SampleNamess (refer to 4.3.1. for a description of the variable names). The specimen table should be labeled Specimen_Table.xlsx, and saved in the corresponding Clinical_Specimen folder. This file should always be contained in the <Spath> location with the original slide scans. If the Specimen #s on the slides are pathology numbers or other medical identifiers, as is the case at Johns Hopkins, this location should be HIPAA compliant. In this case, once the all slides in the project are done scanning, move this onto OneDrive. The file has the following columns:

Patient #, Specimen #, Cut Data, Level, Batch ID, Stain Date, Scan Date

• Patient #: this is the SampleName defined in 4.3.1.
• Specimen #: this the specimen number that is used to identify the patient clinical information
• Cut Date: the date that the slide was cut from the tissue block
• Level: the cut number from the sections cut on that date
• Batch ID: the staining batch the slides was stained with, more details below in 4.4.6..
• Stain Date: the date the slide was stained on
• Scan Date: the date the slide started HPF scanning