_whole_slide_imaging
Clinical Data Table - Whole Slide Imaging
Table Columns
| field | type | required | phi | phi scrubbing operation |
|---|---|---|---|---|
| whole_slide_imaging_id | INT64 | Yes | Yes | Sub Not Stable between Data Refreshes |
| accession_number | STRING | Yes | Yes | Hash |
| specimen | STRING | No | ||
| block | STRING | No | ||
| slide | STRING | No | ||
| person_id | INT64 | Yes | Yes | Sub with Stable between Data Refreshes |
| acquisition_date | DATETIME | No | Yes | Jitter |
| procedure_start_time | DATETIME | No | Yes | Jitter |
| specimen_received_date | DATETIME | No | Yes | Jitter |
| brand | STRING | No | ||
| scanner | STRING | No | ||
| mpp | FLOAT64 | No | ||
| json_uri | STRING | Yes | ||
| tiff_uri | STRING | Yes | ||
| specimen_source_category_value | INT64 | No | ||
| specimen_source | STRING | No | ||
| specimen_type_category_value | INT64 | No | ||
| specimen_type | STRING | No | ||
| spec_task_list | ARRAY<STRUCT<task_c INT64, task_name STRING>> | No | ||
| note_id | INT64 | No | Yes | Sub with Stable between Data Refreshes |
Columns Description
whole_slide_imaging_id (PK)
Primary key for the whole slide imaging table.
accession_number
Accession number from cross walk linking source_deid_slide_id to accession number provided by Roxanna’s Lab, where it also exists in the order_rad_acc_num table and can be linked to the same patient.
specimen
Specimen identifier associated with the slide.
block
Block identifier associated with the slide.
slide
Slide identifier.
person_id (FK)
OMOP person_id associated with the slide.
acquisition_date
Date and time when the slide image was acquired.
procedure_start_time
Date and time when the procedure started from the clarity order_proc table.
specimen_received_date
Date and time when the specimen was received.
brand
Brand of the scanner used to digitize the slide.
scanner
Scanner model used to digitize the slide.
mpp
Microns per pixel resolution of the digitized slide image.
json_uri
GCS URI to JSON metadata for the slide.
tiff_uri
GCS URI to TIFF image for the slide.
specimen_source_category_value
Category value for the specimen source.
specimen_source
Specimen source from the clarity spec_db_main table.
specimen_type_category_value
Category value for the specimen type.
specimen_type
Specimen type from the clarity spec_db_main table.
spec_task_list
Array of specimen task entries, each containing a task category value and task name.
note_id (FK)
Foreign key link to the pathology report in the notes table.