GeoMx Auxiliary Files
A NanoString GeoMx Auxiliary Files entry documents the supporting, non-image and non-count files that accompany a NanoString GeoMx Digital Spatial Profiler (DSP) experiment. Rather than describing the imaging or expression data itself, this module tracks the auxiliary artifacts needed to fully interpret and reproduce a GeoMx run: the ROI/segment annotation file, the PKC probe kit configuration file, the lab worksheet(s) generated during the run, and the DSP config.ini file.
These files are typically produced automatically by the GeoMx DSP instrument and software alongside the imaging and sequencing/count data, but they are easy to overlook when depositing a dataset. Capturing their Synapse identifiers here ensures that anyone reusing the imaging or expression data (Levels 1–3) can also locate the exact probe configuration, worksheet, and run settings that produced it.
Why You Should Contribute NanoString GeoMx Auxiliary Files Entries¶
Contributing auxiliary file entries ensures that the configuration and worksheet files needed to interpret or reproduce a GeoMx DSP run are not lost or disconnected from the primary imaging and expression data, making the full experiment traceable and reusable by others.
Who Should Be Contributing NanoString GeoMx Auxiliary Files Entries?¶
- Core Facility Staff – Deposit the PKC, config, and worksheet files generated directly by the GeoMx DSP instrument.
- Spatial Biology Researchers – Ensure auxiliary files are linked to the correct experiment and biospecimens they support.
- Computational Analysts – Confirm that the probe kit and configuration files needed to reprocess or validate results are available and correctly referenced.
- Data Managers – Track auxiliary file completeness alongside the imaging and expression data deposited for a study.
Download Template¶
You can download the NanoStringGeoMxAuxiliaryFiles 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 |
|---|---|---|---|---|---|---|---|
| NanoStringGeoMxAuxiliaryFiles_id | Unique row identifier, used as a primary key for record updates. This should be equivalent to the file Synapse Id unless otherwise indicated. | True | string | None | ^syn\d{7,8}$ | None | |
| Synapse ID of GeoMx DSP ROI Segment Annotation File | Synapse ID(s) for ROI/AOI/Segmentation annotations in the GeoMx DSP experiment. | False | string_list | None | ^syn\d{7,8}$ | None | |
| Synapse ID of GeoMx DSP PKC File | The Synapse ID(s) associated with the PKC mapping file for the assay. Multiple files are listed as comma separated values. | False | string_list | None | ^syn\d{7,8}$ | None | |
| Synapse ID of GeoMx Lab Worksheet File | Synapse ID(s) of Lab Worksheet Files output from the GeoMx DSP workflow. Multiple files are listed as comma separated values. | False | string_list | None | ^syn\d{7,8}$ | None | |
| Synapse ID of GeoMx DSP Config File | Synapse ID of config.ini file generated by the GeoMx DSP workflow. | False | string_list | None | ^syn\d{7,8}$ | None |