Documentation

Import / Export

Import Gating ML Files

In addition to being able to read FCS files, Floreada can read Gating ML files. Gating ML files are a standardized way to represent gate definitions, which theorectically allows for interoperability between different analysis software (although since the standard is basically never implemented correctly or completely, this is often not the case). You can import a Gating ML file exactly like you would load an FCS file, by clicking "File"->"Open File(s)".

Once a Gating ML file is opened in Floreada, it will be displayed as a gating tree in the side panel. Note that since these are just gate definitions and do not contain any event data, they are not viewable in the plot view. However, the gate defined in the file will be displayed in the population tree and they can be drag-and-dropped onto any population that you have open.

If the Gating ML file contain a gate that is not implemented in Floreada, it will be ignored.

Export Gating ML Files

Floreada is also able to export a Gating ML based file which can save any gates that you have created. We add in some extra data to help save more of your workspace, including the gating heirarchies for particular files. To restore your workspace, open both your fcsfile and saved gating ml file.

Note that only certain things are saved in the workspace file. Saved items include:

Notable things that are not currently saved (but will be saved soon after a future update) include:

Export Images

If you would like to save the current plot, you can export the image by going to "File"->"Save Image". In the export popup, there are several options that you can use to customize the image including:

Axis Labels

You can rename the X and Y axis to something other than the parameter name.

Enable/Disable Elements

You can enable or disable the following elements in the image:

Image Size

The exported image is always square but you can set how big you would like it to be in pixels.

Image Batching

The image export popup has a batch option. If you select batch, then all files that have an analogous population to the population that you are exporting with also have their images saved in a zip file.

Export Events CSV

Sometimes it is useful to see the actual values for events in a file. You can export a CSV file which contains the events organized as a table which can be viewed with an excel-like program. All values are the values of Floreada's internal representation of the events which may differ trivially from the values contained within the fcs file. For example, a file may store event values as integers, whereas Floreada stores ALL values as floating point numbers. Therefore there may be a very tiny difference between the two, and if there is a difference it is almost certainly negligable.

EventParam 1Param 2...Param N
01.90.12...0.47
10.031.2...0.38

After clicking "File"->"Export Event CSV File", the popup menu will allow you to name the exported file and select from a few options.

Compensated Events

If the file has a compensation matrix, you can selected this option to export the compensated event values rather than uncompensated values.

Include Event Number

If this option is selected, the event number will be listed in the first column of the exported file (as in the example above).

Export Statistics CSV

In order to facilitate further statistical analysis outside the scope of our software, we have an easy interface to export all of your statistics into a CSV file which can then be imported into an excel-like program.

Custom Name1Custom Name2
FileFull Stat Name1Full Stat Name2
File 110293.99172.12
File 2297.0319273.2