Set up a 3' Transcriptome planned run

Plan a 3' Transcriptome run in ElemBio Cloud so a connected AVITI24™ System can launch it.

Plan the run

1. On the Planned Runs page, select Plan a Run.
2. Select Cell Screening with Cytos.
3. Enter a unique name and, optionally, a description.
4. (Optional) Upload your run manifest CSV. To prepare one, see Cell screening run manifest.
5. Select 12 wells.
6. For Cell Culture Optimization Run, select No.
7. Under Custom Workflow, select your published 3' Transcriptome design.
8. (Optional) Configure advanced run settings.
9. 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.