Exporting and Importing Gates within Cytobank and with Gating-ML


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 page of the receiving experiment and type the name or experiment number of the donor experiment into the Import Gates dialog:

(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 experiment that has Gates that are tailored across Populations, the Population may not be imported. If you note a missing Population after import, go to the Population Manager in the gating interface, create the Population, and choose which Gates define the Population by checking the checkboxes. 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 represents a standard developed by the International Society for Advancement of Cytometry (ISAC) for computer interchangeable and unambiguous XML-based gate definitions. You may also see it written as GatingML or Gating ML

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.


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 > Import > Upload Gates From Gating-ML.

2) From within the Gating page, click Import 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.

Have more questions? Submit a request