GeoMx ROI Segment Annotation
A NanoString GeoMx ROI Segment Annotation entry documents the Region of Interest (ROI) and Area of Illumination (AOI)/segment metadata generated during a GeoMx Digital Spatial Profiler (DSP) run. Each entry reports one assayed biospecimen per row, together with the ROI and AOI names and coordinates, scan- and slide-level identifiers, and quality control status as reported by the GeoMx DSP application.
Beyond spatial location, this module captures the segment-level quality metrics used to assess and normalize GeoMx data: binding density, positive normalization factor, surface area, nuclei count, tissue stain used to select ROI boundaries, and the negative control, no-template-control, and limit-of-quantification values used for background correction. It also carries the sequencing quality metrics (raw, stitched, aligned, deduplicated, and trimmed read counts, coverage, and MapQ30) associated with each segment, linking spatial and sequencing quality control together in a single record.
Why You Should Contribute NanoString GeoMx ROI Segment Annotation Entries¶
Contributing ROI/segment annotation entries ensures that the spatial location, quality control metrics, and normalization factors behind every GeoMx expression measurement are documented and traceable back to the specific biospecimen, ROI, and AOI that produced them.
Who Should Be Contributing NanoString GeoMx ROI Segment Annotation Entries?¶
- Spatial Biology Researchers – Confirm that ROI and AOI selections accurately reflect the biological regions of interest being studied.
- Core Facility Staff – Record the scan, slide, and segment QC metrics reported directly by the GeoMx DSP application.
- Computational Analysts – Ensure normalization factors and QC metrics are complete and correctly linked so downstream expression data can be properly background-corrected and interpreted.
- Data Managers – Track ROI/segment annotations alongside the imaging and sequencing data deposited for a study.
Download Template¶
You can download the NanoStringGeoMXROISegmentAnnotation CSV template to streamline data entry.
Full Field Reference¶
Below is the full field reference table with attributes and their descriptions.
| Attribute | Description | Required | Column Type | Format | Regex Pattern | Standard Terms | Examples |
|---|---|---|---|---|---|---|---|
| NanoStringGeoMXROISegmentAnnotation_id | Unique row identifier, used as a primary key for record updates | True | string | None | None | None | |
| Biospecimen Key | Unique Biospecimen_id foreign key(s) that link metadata entries as part of the same collection. Please provide multiple values as a comma-separated list. | False | string | None | -B\d{1,9} | None | |
| GeoMx Scan name | GeoMx Scan name (as appears in Segment Summary) | True | string | None | None | None | |
| GeoMx ROI Name | Name of Region of Interest corresponding to file. Multiple names should be comma-separated | True | string_list | None | None | None | |
| GeoMx AOI Name | Name of Area of Illumination corresponding to file. Multiple names should be comma-separated | True | string_list | None | None | None | |
| GeoMx Tags | The basename(s) or unique identifier(s) for FASTQ, RCC, or DCC file(s) associated with this ROI. | False | string | None | None | None | |
| GeoMx ROI X Coordinate | Region of Interest X location within the image | False | number | None | None | None | |
| GeoMx ROI Y Coordinate | Region of Interest Y location within the image | False | number | None | None | None | |
| GeoMx AOI X Coordinate | Area of Illumination X location within the image | False | number | None | None | None | |
| GeoMx AOI Y Coordinate | Area of Illumination Y location within the image | False | number | None | None | None | |
| GeoMx QC status | ROI quality control flag as reported by the application | False | string_list | None | None | None | |
| GeoMx Scan Height | Height of the scan for GeoMx Analysis | False | number | None | None | None | |
| GeoMx Scan Width | Width of the scan for GeoMx Analysis | False | number | None | None | None | |
| GeoMx Scan Offset X | Offset X of the scan for GeoMx Analysis | False | number | None | None | None | |
| GeoMx Scan Offset Y | Offset Y of the scan for GeoMx Analysis | False | number | None | None | None | |
| GeoMx Binding Density | The binding density as reported by the application | False | number | None | None | None | |
| GeoMx Positive norm factor | The Positive Control Normalization factor calculated using pos-hyb controls | False | number | None | None | None | |
| GeoMx Surface area | Surface area of the ROI in square microns (µm2) | False | number | None | None | None | |
| GeoMx Nuclei count | Number of nuclei detected in the segment (if applicable) | False | number | None | None | None | |
| GeoMx Tissue Stain | Text description of the stain, fluorescent reporter, or channel used to select the boundaries of the ROI. | False | string | None | None | None | |
| GeoMx Slide name | Similar to a Run ID, the slide name indicates the slide a given ROI is linked to (as reported in Segment Summary). | False | string | None | None | None | |
| NGS Raw Reads | Reads not yet analyzed in any way to be used for data analysis. The number of reads that pass filter from the flow cell represented in the FASTQ file. | False | number | None | None | None | |
| NGS Stitched Reads | Represents consensus from the overlapping sequence of read 1 and 2. This is a % of the aligned reads that were overlapped and consensus confirmed, usually upward of 80% but less in terms of number of reads than aligned reads | False | number | None | None | None | |
| NGS Aligned Reads | Is a sequence that has been aligned to a gene/probe. Typically these reads can number from the hundreds of thousands to tens of millions. In GeoMx alignment is via mapping the RTS ID to a white list of sequences that represent targets. | False | number | None | None | None | |
| NGS Deduplicated Reads | Is the replacement of blocks of duplicate data with a Virtual Index Pointer linking the new sub-block to the existing block of data in a duplicate repository. This is used to reduce the amount of space need to store the data. | False | number | None | None | None | |
| NGS Trimmed Reads | Number of the reads remaining after trimming has been applied. | False | number | None | None | None | |
| NGS Sequencing Coverage | Depth of coverage on assembly used. Found by (Unique Aligned Basecalls)/(Reference Length) | False | number | None | None | None | |
| NGS MapQ30 | Number of reads with Quality >= 30. | False | number | None | None | None | |
| GeoMx Negative count mean | The geometric mean of the unique negative probes in a GeoMx panel that do not target mRNA and establish the background count level per segment | False | number | None | None | None | |
| GeoMx No Template Control count | The number of reads detected by the GeoMx probe panel in the control associated with this ROI. | False | number | None | None | None | |
| GeoMx Excluded Outlier Probes | The list of probes excluded from analysis. | False | number | None | None | None | |
| GeoMx Limit of Quantification | The calculated limit of quantification associated with the segment. | False | number | None | None | None |