Requirement level: recommended
This table is highly recommended and it is designed to provide quality metrics for the Spot localization, information about the optical Channel that was used to image the Spot, and various aberration corrections that have been applied prior to localization (e.g., drift correction, chromatic correction, etc.).
Because the metrics used to quantify Spot detection accuracy and precision are not trivial and lacking a widely shared consensus, the specific columns in this table remain largely at the user’s discretion and should be described with sufficient details to ensure interpretation and reproducibility.
However, in order to align with existing 4DN-BINA-OME Microscopy Metadata specifications, the use of specific column names and descriptions is conditionally required in case the described metric is reported. As an example, the column name X_Drift is conditionally required in case the user intends to report a comparison between the Observed vs. Expected (i.e., based on a fiducial reference) positions of a detected Spot.
The table is indexed by Spot_ID and each row corresponds to a DNA or RNA bright Spot. The order of all other columns (including those conditionally required) and of the rows are at the user's discretion.
Spot fit quality
- The first line in the header is always "##FOF-CT_version=vX.X"
- The second line in the header is always "##Table_namespace=4dn_FOF-CT_quality"
The header MUST contain a mandatory set of fields that describe any algorithm that was used to produce/process data in this table. In case more than one algorithm were used, please use the same set of fields for each of them.
The header MUST include a detailed description of each optional columns used.
As with all other Spot Data tables in this format, each row corresponds to data associated with an individual Spot.
The first column of this table is always Spot_ID. The content and order of all other columns is largely at user's discretion. However, in order to align with existing Microscopy Metadata specifications, the use of specific column names and descriptions is conditionally required as indicated below. The order of all other columns (including those conditionally requried) and of the rows are at the user's discretion.