Visium RNA Level 4
A 10x Visium RNA Level 4 entry documents further-processed data built from a 10x Visium RNA Level 3 output, capturing the generic workflow type and workflow parameters used to derive higher-order analysis products (e.g., spatial clustering, differential expression, or other downstream spatial analyses) from the per-spot summary data.
As the most highly processed level in the Visium cluster, Level 4 entries emphasize workflow provenance, ensuring that the analysis choices behind a derived spatial result remain traceable back through Level 3, Level 2, and Level 1 to the original tissue and sequencing run.
Why You Should Contribute 10x Visium RNA Level 4 Entries¶
Contributing 10x Visium RNA Level 4 entries ensures that downstream spatial analysis outputs remain traceable to the workflow and parameters that produced them, supporting reproducibility for results shared through the CCKP.
Who Should Be Contributing 10x Visium RNA Level 4 Entries?¶
- Computational Genomics Analysts – Document the workflow type and parameters used to generate derived spatial analysis products.
- Spatial Biology Researchers – Confirm that derived results are correctly linked back to the Level 3 data they were built from.
- Bioinformatics Pipeline Developers – Track workflow versions to support reproducibility across pipeline updates.
- Data Managers – Maintain consistent, portal-ready metadata for derived Visium analysis outputs shared through the CCKP.
Download Template¶
You can download the VisiumRNALevel4 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 |
|---|---|---|---|---|---|---|---|
| 10xVisiumRNALevel4_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 | |
| 10xVisiumRNALevel3 Key | Unique 10xVisiumRNALevel3_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 | |
| 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 | |
| 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 | |
| Visium Workflow Type | Generic name for the workflow used to analyze the visium data set. | True | string | None | None | None | |
| Visium Workflow Parameters Description | Parameters used to run the workflow. | True | string | None | None | None |