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 cytoprofiling runs. Available charts and metrics are based on the run setup and 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 |
|---|---|---|---|
| Assigned | AVITI OS v3.0.0+ | Percent of all reads that are assigned to a target | Percentage |
| Cell Confluency | AVITI OS v3.0.0+ | Percent of flow cell surface area that is covered by cells | Percentage |
| Cell Count | AVITI OS v3.0.0+ | Number of cells that are 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 in real-time throughout the run.
For each chart, you can expand the view or export the chart as an image.
| Chart | AVITI OS Version | Batch Type | Description |
|---|---|---|---|
| Assignment | AVITI OS v3.0.0+ | Protein | Displays the percentage of reads that are assigned to a target in each batch, and includes the percentage of reads that are a perfect match and the percentage with at least one basecall mismatch |
| Differential Expression Level | AVITI OS v3.0.0+ | Protein or Transcript | Heat map that displays expression levels for targets in each batch relative to other wells |
| Quality Controls | AVITI OS v3.0.0+ | Protein | Bar chart that shows the average count of quality control targets per cell in each protein batch |
| Thumbnails | AVITI OS v3.4.0+ | N/A | A snapshot of the flowcell taken at the beginning of the run, per well. The image indicates cell membrane and nuclear cell paint, and provides a quality check to identify flow cell and seeding quality. |
| Custom Antibody Count | AVITI OS v3.4.0+ | Protein | (For antibody screening runs only) Bar chart that shows the count per cell and includes the well location and custom antibody name, if provided in the run manifest |
| Nuclear Fraction | AVITI OS v3.4.0+ | Protein | (For antibody screening runs only) Bar chart that shows the fraction of each custom antibody in the cell location (nucleus, total) |
| Target Assignment Metrics | AVITI OS v3.4.0+ | Direct In Sample Sequencing (DISS) | (For Teton Atlas™ runs with target to cell assignment) Polony, cell, and target statistics, per target site |