Run Planning for Cytoprofiling

Planned runs allow team members to create and manage runs in ElemBio Cloud for use on any connected AVITI System. A team member can plan a run in ElemBio Cloud, then select it during run setup. The Planned Runs table displays saved configuration information for planned runs. You can only edit or delete planned runs through ElemBio Cloud.

Run Progression

After an instrument starts processing a planned run, the following rules apply:

• During the run setup and before priming begins, the status of a planned run appears as In Use.
• If you discard a planned run before priming, the In Use status is removed and the run becomes available for selection on the instrument.
• After priming, the run moves from the Planned Runs table to the Active Runs and All Runs pages.
• If you discard the run or the run fails after priming, the run is no longer available as a planned run. To make the run available again, you must re-create the planned run.

Compatibility

Cytoprofiling planned runs only appear in AVITI OS if they are compatible with the AVITI System. When you add or edit a planned run, a statement at the bottom of the form identifies the run compatibility requirements.

Planned Run Configuration	Compatible AVITI OS Version	Compatible AVITI Systems	Add-On Requirement
Teton Cartridge, Human MAPK & Apoptosis or Teton Cartridge, Human MAPK & Cell Cycle	3.0.0+	AVITI24	No add-on required
Teton Cartridge and fixed panels	3.3.0+	AVITI24	No add-on required
Custom Add-On Protein	3.3.0+	AVITI24	No add-on required
Small Cell	3.3.0+	AVITI24	No add-on required

Add a Planned Run

1. On the Planned Runs page, select Plan a Run.
2. Select Cytoprofiling with Teton.
3. Enter a unique name.
4. If you have prepared a run manifest, then upload the CSV file.
5. (Optional) Enter a description for your planned run.
6. Select the Well Layout.
7. Select the Cartridge. If you select the Teton Cartridge, then select the Fixed Panel, and optionally select the Custom Add-On Protein.
8. (Optional) For Small Cell, select Yes or No.

   Select Yes to reduce the density of target counts per cell and prevent oversaturation of polonies. Use when all cells in all wells have a diameter ≤ 15 µm and the nucleus is large relative to cell size. Example cell lines to use this setting with are Jurkat, PBMC, MCF-7, PC-3, and HCT-116.

9. Select Save Run.

   ElemBio Cloud saves the run, which appears in the Cytoprofiling Planned Runs table.

Run Manifest Validation

When you add or edit a planned run, ElemBio Cloud validates any attached run manifest. Validation ensures that the run manifest is compatible with the planned run setup. If the run manifest contains mistakes or invalid data, then ElemBio Cloud displays a list of errors and warnings.

You can save a planned run with warnings, but not with errors. Before you proceed, resolve the errors and re-upload the run manifest. For more information on how to set up a cytoprofiling run manifest, see the Run Manifest Documentation.

Edit a Planned Run

1. On the Planned Runs page, locate the run that you want to edit.
2. Select the Run Name. Or, in the Actions column, select More, and then select Edit.
3. Update the run information as needed.
4. Select Save Run.

Delete a Planned Run

1. On the Planned Runs page, locate the run that you want to delete.
2. In the Actions column, select More, and then select Delete.
3. When prompted, enter the name of the planned run.
4. Select Delete to immediately remove the run.