Cytoprofiling Metrics and Charts
ElemBio Cloud displays initial estimates for metrics and charts that AVITI OS generates. The following sections describe the metrics and charts available in ElemBio Cloud for cytoprofling runs. Available charts and metrics depend on the run setup and the version of AVITI OS that the run uses. To compute final metrics for a run, execute Cells2Stats in the cloud or locally.
Cytoprofiling Run Metrics
| Metric | AVITI OS Version | Description | Value |
|---|---|---|---|
| Assignment | AVITI OS v3.0.0+ | Percent of all reads assigned to a target | Percentage |
| Cell Confluency | AVITI OS v3.0.0+ | Percent of flow cell surface area covered by cells | Percentage |
| Cell Count | AVITI OS v3.0.0+ | Number of cells identified in cell segmentation | Thousands of cells |
Cytoprofiling Run Charts
Run charts are available on the Primary Analysis tab of a Run Details page. Run charts display metrics as they appear throughout the run.
For each chart, you can expand the view or export the chart as an image.
| Chart | AVITI OS Version | Description |
|---|---|---|
| Differential Expression Levels | AVITI OS v3.0.0+ | Heat map displaying expression levels for targets in each batch relative to other wells |
| Assignment | AVITI OS v3.0.0+ | Displays the percent of reads assigned to a target in each batch, including the percent of reads that are a perfect match and the percent with at least one basecall mismatch |
| Quality Controls | AVITI OS v3.0.0+ | Bar chart showing the average count of quality control targets per cell in each batch |