Optimization run
Plan and run a Cytos™ Onboard Cell Culture Optimization run on AVITI24™.
What an optimization run captures is on the optimization run overview.
Set up a planned run
- On the Planned Runs page, select Plan a Run.
- Select Cell Screening with Cytos.
- Enter a unique name and, optionally, a description.
- (Optional) Upload your run manifest CSV. To prepare one, see Cell screening run manifest.
- Select 12 wells.
- For Cell Culture Optimization Run, select Yes.
- (Optional) Configure advanced run settings.
- Select Save Run.
Advanced run settings
The following settings are optional and available under Advanced Run Settings.
Custom recipe
To use a custom recipe that is not available in Custom Designer, browse and import a recipe file from a USB drive.
A custom recipe is a recipe file (.rec) provided by Element Biosciences, or an available Element recipe that you select instead of uploading a file. Leave this field blank to use the default recipe for your selected kit. Some Element recipes have restrictions based on the selected kit.
Save raw imaging projections
For Save Raw Imaging Projections, the default setting is Yes.
Save raw imaging projections saves the original Cell Paint and protein image projections captured from the flow cell. The system saves these projections before image processing, normalization, or background correction. This setting adds 50–100 GB to the run output.
Save per target background images
For Save Per Target Background Images, the default setting is No.
The system always captures a background image before applying any dyes, to measure autofluorescence and baseline background intensity. Selecting Yes additionally saves a background image for every imaging target. Those images help track background intensity over time and enable background subtraction. This setting increases both run time and final data output size.
Illumination correction
For Illumination Correction, the default setting is Yes.
Illumination correction estimates extracellular background signal. The system subtracts that signal and corrects for variability in illumination across the field of view.
For generic planned-run actions (edit, clone, delete), see Run planning.
Run monitoring metrics
The AVITI24 System reports the following metrics for optimization runs:
| Metric | Description |
|---|---|
| Thumbnail | Snapshot of the flow cell taken at the beginning of the run, per well. Shows cell membrane and nuclear cell paint for a quality check on flow-cell seeding. |
To monitor a run in progress from ElemBio Cloud, see Remote run monitoring.
Analyzing an optimization run
Compare your well thumbnails against the reference images in the Cell Culture Hub to judge whether confluency is low, ideal, or over. The Cell Culture Hub shows pre-fixation and post-fixation images for several cell lines and plate formats, so you can adjust seeding density and surface coating before your next run.
If confluency does not match the ideal reference images in the Cell Culture Hub, adjust your seeding density or surface coating and repeat the optimization run before you commit reagents to a Cytos protein or RNA assay.
Next steps
Once your cell culture protocol is confirmed, use the same seeding density and surface coating for a Cytos protein or RNA run. Each of the following run types requires a published custom design, so start by reviewing the application guide:
- Protein screening overview: cell paint plus up to 20 custom protein targets.
- 3' transcriptome overview: cell paint plus 3' polyadenylated transcripts, with an optional protein add-on.
- Optical pooled screening overview: cell paint plus guide RNA barcodes read optically from a pooled CRISPR screen, with an optional protein add-on.
- Multimodal pooled screening overview: cell paint plus guide RNA and 3' transcripts from the same cell, with an optional protein add-on.