GeoMx Imaging
A NanoString GeoMx Imaging entry documents the images acquired directly by the GeoMx Digital Spatial Profiler (DSP) instrument during a spatial profiling run. This includes the standard file-level descriptors (format, species, design, assay) shared across the data model, along with GeoMx-specific attributes such as the imaging channel names captured and the Synapse ID(s) of tabular files containing the coordinate points for each Area of Illumination (AOI) found in the image.
Because GeoMx images can vary widely in acquisition hardware and configuration, this module also captures detailed instrument- and file-format-level imaging metadata: platform model and manufacturer, acquisition software, objective and magnification, working distance, immersion type, field-of-view size and index, physical pixel size and dimension order, bit depth, plane count, and timepoint/z-stack structure. Imaging entries link forward to the sequencing outputs derived from the same run (Level 1 and Level 2) and to the ROI/segment annotations and biospecimen that were imaged, anchoring the full GeoMx data provenance chain.
Why You Should Contribute NanoString GeoMx Imaging Entries¶
Contributing imaging entries ensures that the raw scan images underlying a GeoMx DSP experiment are properly cataloged with the acquisition and instrument details needed to interpret them, and are traceable to the ROIs, segments, and downstream expression data they informed.
Who Should Be Contributing NanoString GeoMx Imaging Entries?¶
- Core Facility Staff – Record the instrument, software, and acquisition settings used to capture GeoMx scan images.
- Spatial Biology Researchers – Confirm imaging metadata accurately reflects the tissue, channels, and regions profiled.
- Computational Imaging Analysts – Ensure channel names and AOI coordinate files are correctly linked so downstream expression data can be traced back to specific image regions.
- Data Managers – Track imaging files as they are deposited alongside sequencing and annotation data for a study.
Download Template¶
You can download the NanoStringGeoMxDSPImaging 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 |
|---|---|---|---|---|---|---|---|
| NanoStringGeoMxDSPImaging_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 | |
| Filename | The path of a file in Synapse, relative to the project. The file associated with the path will be annotated with attributes contained in this sheet. | False | string | None | None | None | |
| NanoStringGeoMxDSPLevel1 Key | Unique NanoStringGeoMxDSPLevel1_id foreign key(s) that link metadata entries as part of the same Dataset. Please provide multiple values as a comma-separate list. | False | string | None | None | None | |
| NanoStringGeoMxDSPLevel2 Key | Unique NanoStringGeoMxDSPLevel2_id foreign key(s) that link metadata entries as part of the same Dataset. Please provide multiple values as a comma-separate list. | False | string | None | None | None | |
| NanoStringGeoMxAuxiliaryFiles Key | Unique NanoStringGeoMxAuxiliaryFiles_id foreign key(s) that link metadata entries as part of the same Dataset. Please provide multiple values as a comma-separate list. | False | string | None | None | None | |
| NanoStringGeoMXROISegmentAnnotation Key | Unique NanoStringGeoMXROISegmentAnnotation_id foreign key(s) that link metadata entries as part of the same Dataset. Please provide multiple values as a comma-separate list. | False | 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 | |
| Study Key | The unique Study_id foreign keys associated with the resource, found in the grant Study information. Used to group the resource with other components. Please provide multiple values as a comma-separated list. | False | string | None | None | None | |
| DatasetView Key | Unique DatasetView_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 | None | None | |
| File Alias | A string identifier associated with the file. Must be unique. Can be the repository accesssion number (e.g., Synapse ID, GEO identifier such as GSE12345). No Greek Letters or DOIs. | True | string | None | None | None | |
| File Description | Description of the file. | False | string | None | None | None | |
| File Design | The overall design of the dataset or file, including a batch identifier, if applicable. | False | string | None | None | None | |
| File Level | The processing level the file can be mapped to. | True | string | None | None | View | |
| File Assay | The assay the file is representative of. | True | string | None | None | View | |
| File Species | The species the data was collected on. | True | string | None | None | View | |
| File Url | The url of where the file is stored. | True | string | uri | None | None | |
| File Format | The format of the file described by this entry. | True | string | None | None | View | |
| File Data Use Codes | DUO code - A data item that is used to indicate consent permissions for datasets and/or materials, and relates to the purposes for which datasets and/or material might be removed, stored or used. Available DUO code definitions can be found here: https://mc2-center.github.io/data-models/valid_values/study/#attribute-study-data-use-codes | False | string_list | None | None | None | |
| File Longitudinal Group | A label that can be used to identify groups of files from the same longitudinal/time-resolved experiment | False | string | None | None | None | |
| File Longitudinal Event Type | The type of event to which File Longitudinal Total Time Elapsed is related | False | string | None | None | View | |
| File Longitudinal Sequence Identifier | The order in which this file was collected with respect to the longitudinal experiment (e.g., 1, 2, etc.). Integer. | False | number | None | None | None | |
| File Longitudinal Time Elapsed Unit | The unit of time associated with Sequential and Total Time Elapsed attributes. | False | string | None | None | None | |
| File Longitudinal Total Time Elapsed | The total time elapsed between the first and current files contained this longitudinal group. | False | number | None | None | None | |
| GeoMx Imaging Channel Names | Name(s) of imaging channel(s) associated with the image; multiple values should be provided as a comma-separated list. | False | string_list | None | None | None | |
| GeoMx Imaging AOI Coordinates | Synapse Id(s) of tabular file(s) containing coordinate points for AOIs found in the image; multiple values should be provided as a comma-separated list. | False | string_list | None | None | None | |
| ImagingChannel Key | Unique ImagingChannel_id foreign key(s) that link metadata entries as part of the same Dataset. Please provide multiple values as a comma-separate list. | False | string | None | None | None | |
| Image Assay Type | Type of imaging assay | True | string | None | None | View | |
| Image Protocol Link | Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated. | False | string | uri | None | None | |
| Image Platform Model | The specific model of the instrument used to carry out an imaging experiment. | False | string | None | None | None | |
| Image Platform Manufacturer | Producer of the imaging equipment that was used to generate the digital image | False | string | None | None | None | |
| Image Software | The name of the software package that was used to capture, generate, and process the image. | False | string | None | None | None | |
| Image Objective | Objective lens identifier | False | string | None | None | None | |
| Image Nominal Magnification | The magnification of the lens as specified by the manufacturer - i.e. '60' is a 60X lens. floating point value > 1(no units) | False | number | None | None | None | |
| Image Lense Aperture | The numerical aperture of the lens. Floating point value > 0. | False | number | None | None | None | |
| Image Working Distance | The working distance of the lens, expressed as a floating point number. Floating point > 0. | False | number | None | None | None | |
| Image Working Distance Unit | The units of the working distance. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um) | False | string | None | None | View | |
| Image Immersion Type | Immersion medium | False | string | None | None | View | |
| Image Pyramidal | Does data file contain pyramid of images | False | boolean | None | None | View | |
| Image Z stack | Does data file contain a Z-stack of images | False | boolean | None | None | None | |
| Image Timeseries | Does data file contain a time-series of images | False | boolean | None | None | None | |
| Image FOV Index | Index of FOV (as it pertains to its sequence order). Integer >= 1 | False | number | None | None | None | |
| Image FOV Size X | Field of view X dimension. Floating point | False | number | None | None | None | |
| Image FOV Size X Unit | Field of view X dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um) | False | string | None | None | None | |
| Image FOV Size Y | Field of view Y dimension. Floating point value | False | number | None | None | None | |
| Image FOV Size Y Unit | Field of view Y dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um) | False | string | None | None | None | |
| Image Frame Averaging | Number of frames averaged together (if no averaging, set to 1). Integer >= 1 | False | number | None | None | None | |
| Image Identifier | Unique internal image identifier. eg "Image:0". (To be extracted from OME-XML) | False | string | None | None | None | |
| Image Dimension Order | The order in which the individual planes of data are interleaved. | False | string | None | None | None | |
| Image Physical Size X | Physical size (X-dimension) of a pixel. Units are set by PhysicalSizeXUnit. Floating point value > 0. | False | number | None | None | None | |
| Image Physical Size X Unit | The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um) | False | string | None | None | None | |
| Image Physical Size Y | Physical size (Y-dimension) of a pixel. Units are set by PhysicalSizeYUnit. Floating point value > 0. | False | number | None | None | None | |
| Image Physical Size Y Unit | The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um) | False | string | None | None | None | |
| Image Physical Size Z | Physical size (Z-dimension) of a pixel. Units are set by PhysicalSizeZUnit. Floating point value > 0. | False | number | None | None | None | |
| Image Physical Size Z Unit | The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um) | False | string | None | None | None | |
| Image Pixels BigEndian | Boolean (True/False) | False | boolean | None | None | View | |
| Image Plane Count | Number of Z-planes (not to be confused with downsampled "pyramid"). Integer >=1 | False | number | None | None | None | |
| Image Channel Size | Number of channels. Integer >= 1 | False | number | None | None | None | |
| Image Number of Timepoints | Number of time points. Integer >= 1 | False | number | None | None | None | |
| Image X Pixels | Size of image: X dimension (in pixels). Integer >= 1 | False | number | None | None | None | |
| Image Y Pixels | Size of image: Y dimension (in pixels). Integer >= 1 | False | number | None | None | None | |
| Image Z Pixels | Size of image: Z dimension (in pixels). Integer >= 1 | False | number | None | None | None | |
| Image Pixel Type | Data type for each pixel value. E.g. "uint16" | False | string | None | None | None |