Visium RNA Level 3
A 10x Visium RNA Level 3 entry documents processed spatial transcriptomics data built from a 10x Visium RNA Level 2 alignment together with its associated auxiliary files. This level captures per-spot summary statistics such as spots under tissue, mean reads per spatial spot, median genes and UMI counts per spot, sequencing coverage, and the proportion of reads mapped overall and to the transcriptome, along with the workflow version and file type generated.
These per-spot quality and summary metrics are what allow downstream users to assess the technical performance of a Visium run (e.g., tissue coverage, sequencing depth per spot) before interpreting the underlying biology.
Why You Should Contribute 10x Visium RNA Level 3 Entries¶
Contributing 10x Visium RNA Level 3 entries ensures that per-spot quality and summary metrics from a Visium run are documented, giving downstream users the information needed to assess data quality before further spatial analysis shared through the CCKP.
Who Should Be Contributing 10x Visium RNA Level 3 Entries?¶
- Computational Genomics Analysts – Record per-spot summary statistics and workflow versions produced by processing pipelines.
- Spatial Biology Researchers – Confirm that spot-level quality metrics accurately reflect the tissue and capture area analyzed.
- Bioinformatics Pipeline Developers – Document the file types and workflows used to generate processed spatial outputs.
- Data Managers – Maintain consistent, portal-ready metadata for processed Visium sequencing outputs shared through the CCKP.
Download Template¶
You can download the VisiumRNALevel3 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 |
|---|---|---|---|---|---|---|---|
| 10xVisiumRNALevel3_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 | |
| 10xVisiumRNALevel2 Key | Unique 10xVisiumRNALevel2_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 | |
| 10xVisiumAuxiliaryFiles Key | Unique 10xVisiumAuxiliaryFiles_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 | |
| Visium File Type | The file type generated for the visium experiment. | True | 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 | |
| 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 | |
| Visium Spots under tissue | The number of barcodes associated with a spot under tissue. | True | number | None | None | None | |
| Visium Mean Reads per Spatial Spot | The number of reads, both under and outside of tissue, divided by the number of barcodes associated with a spot under tissue. | True | number | None | None | None | |
| Visium Median Number Genes per Spatial Spot | The median number of genes detected per spot under tissue-associated barcode. Detection is defined as the presence of at least 1 UMI count. | True | 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 | |
| Visium Proportion Reads Mapped | Proportion of mapped reads collected from samtools. Number | False | number | None | None | None | |
| Visium Proportion Reads Mapped to Transcriptome | Fraction of reads that mapped to a unique gene in the transcriptome. The read must be consistent with annotated splice junctions. These reads are considered for UMI counting. | True | number | None | None | None | |
| Visium Median UMI Counts per Spot | The median number of UMI counts per tissue covered spot. | True | number | None | None | None |