WARNING
This is a draft under the review by the BBMRI-ERIC Management Committee.
Definition
Scanning, file and annotation attributes: Scan Attributes: Cover various aspects related to the performance and accuracy of Whole Slide Imaging (WSI) systems and scanners.
| Attribute Code | Attribute Name | Description | Data type | Allowed values | Constraints | Cardinality |
|---|---|---|---|---|---|---|
| MIABIS-DIGITALPATHOLOGYSCAN-01 | Scan Identifier | A unique identifier of the scan | String | An ID as a free-text string | none | 0:1 |
| MIABIS-DIGITALPATHOLOGYSCAN-02 | Acquisition Date | The date and time of capturing an image or scanning a glass slide | Date | DATETIME values in ' YYYY-MM-DD hh:mm:ss ' format | Datetime format must be according to ISO 8601. | 0:1 |
| MIABIS-DIGITALPATHOLOGYSCAN-03 | Imaging Protocol | The performed protocol for capturing a digital image | Enumerated values | whole Slide Imaging, slide Microscopy, WSI40XRGB, WSI20XRGB, gross Specimen Imaging, peri-operative Photographic Imaging, other (the value is known but cannot be classified into any of the predefined categories) NULL (the value is unknown) | none | 1:1 |
| MIABIS-DIGITALPATHOLOGYSCAN-04 | Container Condition | Condition of the scanned glass slide and coverslip | Enumerated values | Good, Acceptable, Unacceptable, Subject To Interpretation (The data provider is uncertain whether the container condition is acceptable or unacceptable) | none | 0:1 |
| MIABIS-DIGITALPATHOLOGYSCAN-05 | Device | The vendor-stated name of the equipment or scanner. The attribute should include both the vendor's name and the vendor-stated name of the device. | String | none | 1:1 | |
| MIABIS-DIGITALPATHOLOGYSCAN-06 | Device Software Version | Software and firmware versions of the device used | String | none | 0:1 | |
| MIABIS-DIGITALPATHOLOGYSCAN-07 | Scanning Operation Mode | The scanning procedure used to digitize a glass slide. This attribute does not describe the capabilities of the scanner used for digitization. | Enumerated values | Automatic (digitization without any interference from the personnel responsible), Semi-automatic (digitization with minimal interference from the personnel responsible), Manual (the personnel responsible adjust several parameters during the digitization procedure) | none | 0:1 |
| MIABIS-DIGITALPATHOLOGYSCAN-08 | Z-Stacking | Method of the Z-Stacking, also known as Focus Stacking | Enumerated values | single (one image layer generated by one focal plane in scanning), multiple (n image layers generated by n focal planes in scanning), extended (one image layer generated by the combination of n focal planes in scanning) | none | 0:1 |
| MIABIS-DIGITALPATHOLOGYSCAN-09 | Number of Focal Planes | Number of focal planes along the vertical z-axis used for multiple and extended z-stacking methods | Integer | none | 0:1 | |
| MIABIS-DIGITALPATHOLOGYSCAN-10 | Distance between Focal Planes | Distance between acquisition focal planes given in micrometers (µm) | Decimal | none | 0:1 | |
| MIABIS-DIGITALPATHOLOGYSCAN-11 | Tissue Scan Area | Scanned tissue area given in mm² | Decimal | none | 0:1 | |
| MIABIS-DIGITALPATHOLOGYSCAN-12 | Objective Lens Magnification | The objective lens magnification used for the acquisition of whole slide images. This refers only to the lens magnification and not the final stored image encoded by the spatial resolution attribute. | Enumerated values | 5X, 10x, 20x, 40x, other, NULL | none | 1:1 |
| MIABIS-DIGITALPATHOLOGYSCAN-13 | Spatial Resolution | Dimensions of a pixel in an image, measured in µm | Decimal | none | 1:1 | |
| MIABIS-DIGITALPATHOLOGYSCAN-14 | Illumination Method | Illumination method used for the acquisition of whole slide images | Enumerated values | Transmission Illumination, Reflection Illumination, Epifluorescence Illumination, Brightfield Illumination, Darkfield Illumination, Oblique Illumination, Phase Contrast Illumination, Differential Interference Contrast, Total Internal Reflection Fluorescence | none | 0:1 |
| MIABIS-DIGITALPATHOLOGYSCAN-15 | Illumination WaveLength | Nominal wavelength of the illuminator in nm | Decimal | none | 0:1 | |
| MIABIS-DIGITALPATHOLOGYSCAN-16 | Out-of-Focus Error Rate | Percentage of a scanned area that is out of focus | Decimal | the values should preferably be generated by a (validated) algorithm and encoded as a value between 0 and 1 | 0:1 | |
| MIABIS-DIGITALPATHOLOGYSCAN-17 | Stitching and other Artifact Error Rate | Percentage of a scanned area that is affected by stitching errors or other scanning artifacts | Decimal | the values should preferably be generated by a (validated) algorithm and encoded as a value between 0 and 1 | 0:1 |