Importing

Importing from Other Experiments in CellEngine

Resources from other experiments can be imported, including gates, illustration layouts, channel scales, and compensation matrices.

Howto

1. In the destination experiment’s gating page, click Import….
2. Choose the source experiment, and click Next.
3. Optional: To import gates from your source experiment:
   1. Check the Import populations option.
   2. If the same channel appears in the source and destination experiment, they will automatically be matched. To adjust the mapping of channels between the source and destination experiments, click the drop down and select the destination channel. For example, if you have CD3-PE in the source experiment and CD3-FITC in the destination experiment, you can set the “FITC” row to “PE”.
   3. To skip importing a channel, change Map to channel in to none. Any gates that use channels that are not mapped to a destination experiment channel (marked with ) will not be imported.
4. To continue to illustration import, click Next or Skip.
5. If you imported populations, you can select illustrations from the source experiment you wish to import.
6. Click Next or Skip.
7. If you are importing channels, the scales will be imported by default. Uncheck any of the channels to skip importation, or click the checkbox next to channel to toggle all.
8. Click Next.
9. Select or deselect compensation matrices for importation.
10. Click Import.

Tips

• Copy and paste gates to move the imported gates below a different population in the hierarchy.
• When you import scales, existing gates will be repositioned. Adjustments may be needed.

See also

• Importing FCS files
• Importing annotations
• Duplicating experiments

Importing Experiments from Other Software

Importing from BD FACSDiva™

You can import gates, populations, worksheets, compensations and scales from FACSDiva experiments.

Howto

1. In FACSDiva, right-click on your experiment in the navigator and select Export Experiments. Select an export location, select the directory export option and your experiment name, then click OK. This should create a directory with your FCS files an XML file.
2. In CellEngine, create a new experiment from your inbox.
3. Drag and drop your FCS files and Diva workspace XML file into your browser. Click “Yes” at the prompt asking if you want to import the Diva workspace.

Warning

The Export Experiments function in some versions of Diva exports incorrect FCS files (channels out of order). If this happens, use the Export FCS Files function to export FCS files, and only use the XML file from Export Experiments.

Scale conversion

FACSDiva uses a proprietary implementation of biexponential scaling. When your experiment is imported, your gate coordinates will be converted from the biexponential scales used in your Diva experiment to an ArcSinh scale approximating that biexponential scale, taking into consideration the “below zero” settings for each channel. The imported gates typically have event counts within 1% of the FACSDiva experiment.

FACSDiva calculates biexponential scale values for each individual tube in your experiment. When your experiment is imported, the median of those scale values will be used. If any of your tubes have manual scale values set, then the median of the manual values will be used and the values calculated by Diva will be ignored.

Importing from Cytobank

Experiment information, FCS files, attachments, gates, populations, panels and scales can be imported from Cytobank experiments. Entire accounts can also be imported. Please contact support@cellengine.com for more information.

Statistics between applications are typically identical or almost identical. Events at gate edges are more likely to be different between applications due to differences in numerical precision and rounding.

Population conversion

Cytobank does not use a population hierarchy for gating. Instead, a hierarchy must be inferred based on the gates that comprise your populations. If you have not used the population manager in Cytobank, your gating hierarchy will be step-wise and import seamlessly. However, if you have used the population manager to create, modify or delete populations, there are several conversions to be aware of:

• If more than one gate is different between a population and its next logical descendant, then populations will be automatically created to make the hierarchy step-wise. For example, an experiment with one population comprised of Gate1 and another comprised of Gate1, Gate2, Gate3 has two gates differing between the parent and child populations and is thus not a step-wise hierarchy. During import, a new population comprised of Gate1, Gate2 will be automatically created.

• If a gate is not used in any populations, then a population comprised solely of that gate will be created below Ungated. This is common when you have created readout or signaling gates (e.g. “STAT3+”) that you wish to see on multiple populations. After import into CellEngine, you can copy and paste the gate below the populations where you wish to see it displayed.

Each Cytobank gate can have its own scales. During import, if a gate has scales that are different from the current Cytobank experiment scales, the gate will be transformed to the experiment scales. For more information on this transformation, see changing scales after gating.

Cytobank gates that are tailored per population will be imported as separate populations.

Limitations

• Each Cytobank gate can have its own compensation. CellEngine does not support using different compensations for each gate. Cytobank experiments using multiple compensations are more likely to have differing statistics between applications.