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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 ConfigurationCompatible AVITI OS VersionCompatible AVITI SystemsAdd-On Requirement
Teton™ Cartridge, Human MAPK & Apoptosis or Teton Cartridge, Human MAPK & Cell Cycle3.0.0+AVITI24™No add-on required
Teton run with Custom Add-On Protein with Full Custom Protein Panel3.3.0+AVITI24No add-on required
Teton run with Custom Add-On Protein with Teton Focus Panels3.3.0+AVITI24No add-on required
Teton Cartridge and Fixed Panels3.3.0+AVITI24No add-on required
Small Cell3.3.0+AVITI24No add-on required
Expanded Z3.4.0+AVITI24No add-on required
48-Well3.4.0+AVITI24No add-on required
Custom Recipe3.4.0+AVITI24No add-on required
Teton Atlas™ Custom Workflow3.4.0+AVITI24No add-on required

Add a Planned Run​

Cytoprofiling with Teton​

  1. On the Planned Runs page, select Plan a Run.
  2. Select Cytoprofiling with Teton.
  3. Enter a unique name.
  4. (Optional) Provide a description of your run.
  5. (Optional) If you have a prepared run manifest, upload the CSV file.
  6. Select 48, 12, or 1 well(s).
  7. Select your cartridge.
  8. If you selected Teton Cartridge, select the Fixed Panel.
  9. (Optional) If you selected Teton Cartridge, select the Custom Add-On Protein Panel.
  10. (Optional) In the Small Cell field, select Yes or No.

    (Recommended for AVITI OS 3.3.0 or earlier) 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. Contact Element Biosciences for guidance on cell lines to use with.

  11. (Optional) In the Expanded Z field, select Yes or No.

    Select Yes to increase the depth of imaging in the z-dimension for cells with increased height or a tendency to form dense colonies. Use when cells in all wells have a height ≥ 6 µm or exhibit strong cell-cell adhesion and growth in clusters. Example cell types to use this setting with include: Jurkat, MCF-7, and Hela.

  12. (Optional) To upload a custom recipe, select the Advanced Run Settings drop-down menu, and then upload your custom recipe file.
  13. Select Save Run.

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

Cytoprofiling with Teton Atlas​

  1. On the Planned Runs page, select Plan a Run.
  2. Select Cytoprofiling with Teton Atlas.
  3. Enter a unique name.
  4. (Optional) Provide a description of your run.
  5. (Optional) If you have a prepared run manifest, upload the CSV file.
  6. Select 48, 12, or 1 well(s).
  7. Select your Direct In Sample Sequencing (DISS) workflow.
  8. (Optional) If required by the design, select a Target Cell Assignment Manifest.
  9. (Optional) In the Small Cell field, select Yes or No.

    (Recommended for AVITI OS 3.3.0 or earlier) 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. Contact Element Biosciences for guidance on cell lines to use with.

  10. (Optional) In the Expanded Z field, select Yes or No.

    Select Yes to increase the depth of imaging in the z-dimension for cells with increased height or a tendency to form dense colonies. Use when cells in all wells have a height ≥ 6 µm or exhibit strong cell-cell adhesion and growth in clusters. Example cell types to use this setting with include: Jurkat, MCF-7, and Hela.

  11. (Optional) To upload a custom recipe, select Advanced Run Settings, and then upload your custom recipe file.
  12. Select Save Run.

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

Cytoprofiling with Antibody Screen​

  1. On the Planned Runs page, select Plan a Run.
  2. Select Cytoprofiling with Antibody Screen.
  3. Enter a unique name.
  4. (Optional) Provide a description of your run.
  5. (Optional) To include custom antibodies in your run, add them to a prepared 12-Well or 48-Well Antibody Screening Kit Run Manifest, and upload the CSV file.
  6. Select 48 or 12 wells.
  7. Select one of the following screening assays:
    • Cell Paint + Control Antibodies + Custom Antibodies
    • Cell Paint + Control Antibodies
    • Cell Paint Only
  8. (Optional) In the Expanded Z field, select Yes or No.

    Select Yes to increase the depth of imaging in the z-dimension for cells with increased height or a tendency to form dense colonies. Use when cells in all wells have a height ≥ 6 µm or exhibit strong cell-cell adhesion and growth in clusters. Example cell types to use this setting with include: Jurkat, MCF-7, and Hela.

  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 the three dots (...), 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 the three dots (...), and then select Delete.
  3. When prompted, enter the name of the planned run.
  4. Select Delete to immediately remove the run.
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