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(s) 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 contains 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 hierarchies for particular files. To restore your workspace, open both your FCS file(s) and saved Gating ML file.

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

• Gates and gate structure for fcs files
• Renamed fcs files
• Custom Parameters
• Statistics

Notable things that are not currently saved include:

• Clustering
• Cell Cycle

Import FlowJo Workspace Files

Floreada can import basic FlowJo Workspaces from recent FlowJo versions. You must open both the .wsp file as well as any associated FCS files.

FlowJo has no affiliation was Floreada.io.

Why do gates imported from FlowJo sometimes have slightly different event counts in Floreada.io?

According to their documentation, FlowJo bins events and has a resolution to their gates. This means that events near the exact boundary of a gate may or may not be included in the gate depending on how the data is binned together. Floreada.io, on the otherhand, checks whether the exact event from the cytometer is in the exact gate boundaries that you have drawn or specified. So there may be slight differences between events on the boundaries of the gate but probably not enough to make a significant difference.

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:

• Title
• Axis Labels
• Gates
• Gate Labels
• Legend
• Overlays

Image Size

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

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 negligible.

To export the events, right click on the population in the file tree and select "Export Events".

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.