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Importing and Exporting

Importing Gates, Scales, Illustrations, and Compensation Matrices from Other Experiments in CellEngine

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

Howto

  1. In the destination experiment’s gating page, click Import…. A dialog will open.
  2. Choose the source experiment, and click Next.
  3. To import gates from your source experiment, follow the steps below. Otherwise, click Skip.
    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 alert button) will not be imported.
    4. Click Next.
  4. If you imported populations, you can select illustrations to import. Select any and click Next, otherwise click Skip.
  5. Select scales to import and click Next.
  6. Select compensation matrices to import and click Next.
  7. If you imported populations, you can select saved statistics export settings to import. Select any and click Next, otherwise click Skip.
  8. Click Import.

Tips

See also

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.

Importing from FlowJo

FCS files, gates, populations, and scales can be imported from FlowJo XML files. Please contact support@cellengine.com for more information.

Exporting Gating-ML

CellEngine can export an experiment’s compensations, scales, gates, and populations as a Gating-ML 2.0 XML file.

Howto

  1. On the experiment summary page, click the export Gating-ML button in the Experiment Details pod.
  2. In the dialog box, select global gates to export global gates, or aspecific FCS file to export the gates tailored to that file. (See limitations below for more information.)
  3. Click export. An XML file will be downloaded.

Limitations

The Gating-ML 2.0 format has several limitations to be aware of:

  • There is no standardized way to communicate the name of gates, populations, or compensation matrices (only a unique ID is standardized). CellEngine encodes resource names in a non-standard "name" attribute.
  • There is no standardized way to communicate which gates apply to which FCS files (i.e. gate tailoring). CellEngine lets you either export the global gates, or export the gates for a specific FCS file (including both tailored and non-tailored gates).
  • Gating-ML does not allow detector names and channel names to be the same if compensation is applied. As such, channel names are prefixed with an underscore (“_”) if the experiment’s active compensation is set to a custom compensation matrix.
  • Gating-ML does not support skewed quadrant gates. During export, skewed quadrant gates will be orthogonal.
  • Gating-ML does not support the Boolean xor operator, but this operator can be used via CellEngine's API. During export, xor operators will be converted to a combination of other Boolean operators.