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Exporting and Importing Gates within Cytobank and with Gating-ML

Background  

There are two ways to import gates into a Cytobank experiment. 

1) Import gates from another Cytobank Experiment using the Import Gates Dialog

2) Import and export gates with Gating-ML

 

Note: before moving gates between Cytobank experiments, remember that gates are only visible with the correct configuration of compensation, and channels. If gates cannot be seen after import, the issue can be remedied with instructions in the linked article.

Import gates from an existing Cytobank experiment

Gates can be imported easily between Cytobank experiments. Simply enter the Gating Editor of the receiving experiment and type the name or experiment number of the donor experiment into the Import Gates dialog:

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(use the import gates feature within the gating interface to import gates from another Cytobank Experiment)

 

Note that currently, only a global version of experiment gates can be imported with this feature. When importing gates from an existing experiment that has gates that are tailored across populations or files, the tailored population will not be imported. If you note a missing population after import, go to the Boolean expressions tab in the Gating Editor and create the population using the necessary gates and Boolean operators. Alternatively, use the tailoring options to tailor the gate Per population. Note that all gates are always imported, so you will not have to redraw any gates (just the corresponding population in some cases). Thus, this workflow does not present a problem for ensuring exactness of templated analysis.

To move tailored gates between experiments, use Gating-ML. 

Import / export gates with Gating-ML

Gating-ML 2.0 [1] represents a standard developed by the International Society for Advancement of Cytometry (ISAC) for computer interchangeable and unambiguous XML-based gate definitions.

Gating-ML provides a file that stores a textual representation of gates. This file can be downloaded from a Cytobank experiment and used as a version storage of gates or to upload to a different experiment as a template for transferring gates.

Gating-ML files can be read and altered with a text editor. This is an example of a segment of a Gating-ML file:

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Exporting Gating-ML from a Cytobank Experiment

First make sure your experiment has the most recent version of your gates. After that, export the Gating-ML file from Actions > Export > Export gating-ML.

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Importing Gating-ML into a Cytobank experiment:

Importing a Gating-ML can be accessed in either of two ways:

1) Navigate to the experiment in which you want to import gates. Then import the gates through Actions > Upload > Upload gates from gating-ML.

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2) From within the Gating Editor, click Upload gating-ML.

 

Tailored gates can be transferred via Gating-ML. The tailored gates are associated with file names. If you wish to apply the tailored gates to new files in another experiment, you may export the Gating-ML from the first experiment and open it in a text editor. You can then search the tailored gate locations using the old file name. Once you have located the file name, replace the file name with the new file name. By replacing the file names, the tailored gates are transferred to the new files. This modified Gating-ML can be imported to the new experiment to apply the tailored gates. 

 

References 

  1. Spidlen, Josef et al. “ISAC's Gating-ML 2.0 data exchange standard for gating description.” Cytometry. Part A : the journal of the International Society for Analytical Cytology vol. 87,7 (2015): 683-7. doi:10.1002/cyto.a.22690

*For Research Use Only. Not for use in diagnostic procedures.

 



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