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 open the Load gates functionality. Select the Import from another experiment option and type the name or experiment number of the donor experiment into the Import gates from experiment dialogue. This will load the currently active gate version from the donor experiment.
For an overview of all gate versions that can be loaded in an experiment, see also Gate versioning.
(Use the Import gates from another experiment feature within the Load gates menu in the Gating Editor interface to import gates from another Cytobank experiment.)
Note that any imported gate and population names that share their name with a gate or population that already exists in the destination experiment will receive a suffix containing a version number, e.g. (1).
Currently, only a global version of experiment gates can be imported with this feature. When importing gates from an existing experiment that has either gates that were copied to other populations or gating groups, the resulting population(s) 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 populations, gates and Boolean operators. Alternatively, drag and drop, or copy the gates into the desired populations. Note that all gates are always imported, so you will not have to redraw any gates (just the corresponding population in some cases). If the original experiment included gates with synchronization settings different from sync to all files and sync to all populations, the corresponding gates in the receiving experiment will be set to sync to files within groups and populations within groups, independently of the number of gating groups defined in the experiment. Read the following article to learn more about the sync settings in the Cytobank platform.
If the original experiment includes gating groups, they will be transferred to the receiving experiment together with the gates and populations. Check this article for an overview of using gating groups. To move all gates and populations 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:
Exporting Gating-ML from a Cytobank Experiment
First make sure you have loaded the desired Gate version in your experiment. After that, export the Gating-ML file from Gates > Download Gating-ML.
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 Gates > Upload gates from gating-ML.
2) From within the Gating Editor, open the Load gates menu and select Upload gating-ML. Select a Gating-ML file or drag it into the upload area and select Apply changes.
Gate positioning can be transferred via Gating-ML. The specific location of the gates is associated with file names. If you wish to apply the same location of the 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 target gate 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 gates are transferred with the specific location information linked to the new files. This modified Gating-ML can be imported to the new experiment.
References
- 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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