Import / Export

Gating ML

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, a new pipeline group will be created with the gating tree contained in the file. You can easily apply the gating tree to file by adding the file to the pipeline group by dragging and dropping.

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.

Notable things that are not currently saved include:

• Clustering
• tSNE

FlowJo

In trying to provide as much interoperability and compatibility as possible between different flow cytometry analysis software, we support importing and exporting FlowJo workspaces. Floreada.io has no affiliation with FlowJo or its parent company.

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.

Export FlowJo Workspace Files

Floreada can also partially export a workspace to a FlowJo .wsp file. You must save the .wsp file in the same folder as your associated FCS files in order for FlowJo open all files correctly. Supported elements include:

• Rect gates
• Poly gates
• Quad gates
• Most Boolean gates
• Statistics
• Pipelines (called Groups in FlowJo)
• Compensation matrices
• Transforms
• Basic Custom Parameters (called Derived Parameters in FlowJo) - Note that Floreada custom parameters in pipelines do not export correctly to FlowJo derived parameters in groups. From our testing with FlowJo 10.10, FlowJo is unable to save its own derived parameter groups in a workspace file so we don't believe this is supported currently.

Notable elements that are not currently saved include:

• Ellipse gate - From available documentation, it seems FlowJo converts ellipse gates to a polygon gates internally and then events are evaluated for membership in that gate. In Floreada.io, we evaluate if the event is contained in the ellipse directly. While we work to resolve these differences, ellipse gates are not currently saved in an exported FlowJo workspace.
• Cell Cycle
• Kinetics
• tSNE
• Clustering

Why do gates sometimes have slightly different event counts in Floreada.io compared to FlowJo?

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.

Archival Cytometry Standard Files

This is a standardized file format that combines all aspects of a flow cytometry analysis in one file. These files ends with the ".acs" file extension and are a normal ZIP file. You can unzip them like a normal ZIP file to see their inner components. ACS files can contain the following inner components:

• A Table of Contents (typically named "toc1.xml) which lists all the other files in the archive and what their purposes are.
• All the FCS files for an experiment
• Gating description files - these can consist of gatingML files, or propietary workspace files such as FlowJo .wsp files

The advantage of exporting to an ACS file is that all of your files will be wrapped up in to one easy to manage ZIP file.
The disadvantage is that since the ACS file contains all of your FCS files, it can take up a lot of disk space.

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".

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.