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, a downloadable text file with gate information encoded in it.

Note: before moving gates between Cytobank experiments, remember that gates are only visible with the correct configuration of compensation, scales, 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 Population Manager in the Gating Editor, create the population, and choose which gates define the population by checking the checkboxes. 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. Please see the following section to learn more about how to use Gating-ML to transfer gates between experiments. 

 

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: 

 

To export 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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To import 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 method of transfer is by using file names to map the tailored gate locations. To map a certain set of tailored gates to a different set of recipient files, the Gating-ML file can be opened in a text editor and file names replaced.

 

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


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