Using Definitons

Solution

Use Case

How to implement solution

Note

Apply definition to existing plots manually

To quickly apply and visualize a definition you have created or edited when you do not intend to run a batch or iterate/change between data files in the data list (i.e. all your files are already loaded into the layout).

See the Applying Definition To Existing Plots chapter.

If you then would like to run a batch process or change between data files using this same definition, ensure your Layout Options for definition loading are set to None (see the Selecting the Default Definition to Use When Loading Data chapter).

Set a definition As Default to automatically apply it to data loaded in a layout.

•You would like to run a batch process and/or change between data files using the data list while using a newly defined or customized compensation when loading files

•You would like the compensation/unmixing definition to be applied to any file loaded into that layout

•You would like the compensation/unmixing definition to be saved into the FCS Express layout.

1.Move the definition of interest into the "Created Manually" folder of the Compensation and Unmixing window. If the definition of interest is already in the Created Manually folder, this step is not required.

2.Apply the definition to all plots (see the Applying Definition Matrices chapter)

3.Right click on the definition from the Compensation and Unmixing window and select "Set As Default"

4.Change your Layout Options to use default definition (see the Selecting the Default Definition to Use When Loading Data chapter).

If no Default compensation is available, FCS Express will behave as defined in the Layout Options (see the Selecting Compensation to Use When Loading Data chapter).

Export definition as an *.allcompensation or *.allunmixing file to apply it to all data files within a folder.

•You would like to run a batch process and/or change between data files using the data list while using a newly defined or customized compensation/unmixing definition.

•You would like the compensation/unmixing definition to be associated with all files within a folder.

•You would like the compensation/unmixing definition to exist independently of the layout (i.e. the definition will be saved into the same folder as the data files.

1.Export the defintiion of interest as *.allcompensation or *.allunmixing file using the Export the selected transformation button of the Compensation and Unmixing window. Be sure to select *.allcompensation (or *.allunmixing) as output file format and to save the definition in the same folder as the data files.

2.Ensure your Layout Options for definition loading are set accordingly (see the Selecting the Default Definition to Use When Loading Data chapter).

3.Create a new layout or open a template (i.e. a layout saved with unlinked data), and load your files into it.

If FCS File or FCS File, then Compensation Default is specified as the default Option for loading definitions, when loading a data file, FCS express will look in the folder where the file is being loaded from for a *.allcompensation or a *.allunmixing file. If the *.allcompensation or the *.allunmixing file is found, that definition is used.

If a file-specific definition is also found (see below) the file-specific definition will be used instead.

If neither a file-specific compensation nor the *.allcompensation matrix is found, FCS Express will behave as defined in the Layout Options (see the Selecting Compensation to Use When Loading Data chapter).

Note: Only 1 *.allcompensation or 1 *.allunmixing definition file should be present in a folder. If  two or more definitions files exist in the same folder, e.g., type1.allcompensation and type2.allcompensation, type3.allunmixing, FCS Express will pick one at random.

Export and assign definition to specific files by saving it as filename.compensation or filename.unmixing file

•You would like to run a batch process and/or change between data files using the data list while using a newly defined or customized compensation/unmixing definition.

•You would like the compensation/unmixing definition to be associated with specific files.

•You would like the compensation/unmixing definition to exist independently of the layout and only apply to the assigned file.

1.Export the definition of interest using the Assign this compensation/unmixing to a data file button of the Compensation and Unmixing window.The filename.compensation (or filename.unmixing) file will be autoamtically saved in the same folder as the data files.

2.Ensure your Layout Options for definition loading are set accordingly (see the Selecting the Default Definition to Use When Loading Data chapter).

3.Create a new layout or open a template (i.e. a layout saved with unlinked data), and load your files into it.

If FCS File or FCS File, then Compensation Default is specified as the Default Definition to Use when Loading Files, when loading a data file, FCS express will look in the folder where the file is being loaded for a file with the same name, but ending in .compensation (or .unmixing). For instance, if you are loading sample1.fcs then FCS Express will look for sample1.fcs.compensation or sample1.fcs.unmixing. If a match is found, FCS Express will load the definition matrix as if it was specified by the .fcs file itself.

If FCS Express does not find the specific definition file, it will look for an *.allcompensation (or *.allunmixing) file (see above) in the same folder as the data file. If present, the definitio in the *.allcompensation (or *.allunmixing) file will be applied to all of the files in that folder.

If neither the file-specific, or the *.allcompensation/*.allunmixing matrix is found, FCS Express will use compensations defined in the Layout Options (see the Selecting the Default Definition to Use When Loading Data chapter).