Visium Auxiliary Files
A Visium Auxiliary Files entry documents supporting data associated with 10x Genomics Visium spatial transcriptomics experiments, such as aligned tissue images, quality control reports, and other files that accompany the primary sequencing and expression outputs of a Visium run. Rather than representing a sequencing or expression level itself, this module links auxiliary artifacts, such as slide images, scale factor files, and QC reports, back to the Visium RNA Level 1 through 4 files, biospecimen, and study they belong to, along with the run, slide, and capture area they were generated from.
Auxiliary files are often what make a Visium dataset interpretable and reusable: tissue images and QC reports give downstream users the context needed to evaluate spot detection, alignment quality, and tissue morphology alongside the expression data.
Why You Should Contribute Visium Auxiliary Files Entries¶
Contributing Visium Auxiliary Files entries ensures that the images, scale factors, and quality control artifacts generated during a Visium run are discoverable and properly linked to the sequencing and expression data they support, giving downstream users full context for interpreting spatial results shared through the CCKP.
Who Should Be Contributing Visium Auxiliary Files Entries?¶
- Spatial Biology Researchers – Document tissue images and slide/capture area context generated during a Visium experiment.
- Computational Genomics Analysts – Record QC reports and scale factor files produced alongside spatial expression processing.
- Sequencing Core Staff – Track which auxiliary files correspond to which Visium run and biospecimen.
- Data Managers – Maintain consistent, portal-ready metadata for auxiliary spatial transcriptomics files shared through the CCKP.
Download Template¶
You can download the VisiumAuxiliaryFiles 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 | CDE | Examples |
|---|---|---|---|---|---|---|---|---|
| VisiumAuxiliaryFiles_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 | CDE:11284037, CRDC_CDE:11284037 | |
| VisiumRNALevel1 Key | Unique VisiumRNALevel1_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 | ||
| VisiumRNALevel2 Key | Unique VisiumRNALevel2_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 | ||
| VisiumRNALevel3 Key | Unique VisiumRNALevel3_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 | ||
| VisiumRNALevel4 Key | Unique VisiumRNALevel4_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 | CDE:11280338, CRDC_CDE:11280338 | |
| File Design | The overall design of the file. | False | string | None | None | None | ||
| File Batch Identifier | An identifier for the batch or group of files processed together (e.g. an extract batch, library prep batch, or sequencing run), used to support downstream analysis of batch effects. Free text, not a fixed list. | False | string | None | None | None | ||
| File Level | The processing level the file can be mapped to. | True | string | None | None | View | ||
| Assay | The assay the dataset, file, or publication is representative of. Multiple values permitted, comma separated. | True | string_list | None | None | View | ||
| Species | The species of origin corresponding to the model, or from which the biospecimen originates. | True | string_list | None | None | View | ||
| Tissue | Tissue type(s) associated with the dataset, file, or publication. Multiple values permitted, comma separated. | False | string_list | None | None | View | ||
| Tumor Type | The tumor type(s), if applicable, associated with the dataset, file, or publication. Multiple values permitted, comma separated. | False | string_list | None | None | View | ||
| File Url | The url of where the file is stored. | True | string | uri | None | None | CDE:11556141 | |
| File Format | The format of the file described by this entry. | True | string | None | None | View | CDE:11416926, CRDC_CDE:11416926 | |
| File Assay Category | The broad category of experimental method used to generate the file, per NCI caDSR CDE 12373576 (Research Activity Experimental Method Type). | False | string | None | None | View | CRDC_CDE:12373576 | |
| 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/shared/#attribute-data-use-codes | False | string_list | None | None | View | CDE:0002001 | |
| 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 (e.g. Enrollment, Baseline). Free text, not a fixed list. | False | string | None | None | None | ||
| File Longitudinal Sequence Identifier | The order in which this file was collected with respect to the longitudinal experiment (e.g., 1, 2, etc.). | False | string | 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 | ||
| Visium Run ID | A unique identifier for this individual run (typically associated with a single slide) of the spatial transcriptomic processing workflow. | True | string | None | None | None | ||
| Visium File Type | The file type generated for the visium experiment. | True | string | None | None | View | ||
| Visium Slide ID | For Visium, it is the unique identifier printed on the label of each Visium slide. The serial number starts with V followed by a number which can range between one through five and ends with a dash and a three digit number, such as 123. For CosMx, this refers to the loaded Flow Cell ID. For Xenium, this ID indicates the slide orientation, as it matches the relative location of the ID on the physical Xenium slide. | True | string | None | None | None | ||
| Visium Capture Area | Area (or Capture Area) - One of the either four or two active regions where tissue can be placed on a Visium slide. Each area is intended to contain only one tissue sample. Slide areas are named consecutively from top to bottom: A1, B1, C1, D1 for Visium slides with 6.5 mm Capture Area and A, B for CytAssist slides with 11 mm Capture Area. Both CytAssist slides with 6.5 mm Capture Area and Gateway Slides contain only two slide areas, A1 and D1. | False | string | None | None | View | ||
| Workflow Version | Major version of the workflow (e.g. Cell Ranger v3.1) | False | string | None | None | None | ||
| Workflow Link | Link to documentation or webpage associated with the computational workflow used to generate the file. | False | string | uri | None | None |