4.1  Flow Cytometry

FCS files are text files produced by Flow Cytometers. Catalyzer is able to extract laser, parameter, and event information from FCS files. It is also able to create dotplots comparing two parameters and histograms of multiple parameters from single or multiple experiment files. At import time the metadata is added to Catalyzer. You can then choose which data to graph and add those graphs to the imported records.

Example FCS data imported

Example FCS Dotplot

Example FCS Histogram

Dotplots and Histograms are created and saved as records with class names "FCS Dotplot" and "FCS Histogram". Modifying these records to create new charts requires the use of the Chart Editor which is launched with the chart icon located at the far right of the chart file name ("FCS Histogram" or "FCS Dotplot" field label).

When an FCS file is imported, two empty charting records are created under the "Dataset 1" folder. These are named based on the FCS file and intended to serve as example records that can be immediately edited to construct initial charts for that file. Like any record in Catalyzer, these charting records can be moved anywhere within the catalog tree and new records can be created with the "Add using Class" menu choice. Unlike other records in Catalyzer, these records should only be edited using the Chart Editor and their class definition should not be modified.

Use the Chart button to start the FCS Chart Editor

The FCS Chart Editor lets you set the parameters you want to plot

The following values are defined using the Chart Editor.

• Chart title The title of the chart. This also determines the name of the image file that is created when the chart record is saved.
• File 1, 2, ... Names of FCS files whose data is being charted.
• Parameter 1, 2, ... Parameter names from the corresponding FCS file that represent the event parameters being charted (for histograms only).
• X parameter The parameter to plot on the X axis.
• Y parameter The parameter to plot on the Y axis.
• Max events to plot The maximum number of events to sample from the file and place on the plot. Smaller values of this parameter may improve the Chart Editor performance.
• Save chart image file to The folder onyour computer in which the chart image file will be saved. The default folder is the location of the FCS file, but any writable folder may be used. Invalid folders will cause the Chart Editor to fail when attempting to save the record and corresponding chart image file.
• Chart size in record The size of the chart image as it appears in the record. Either Small or Large.

Chart display and saving is controlled by the following buttons.

• Draw Chart Draws the chart based on the defined parameters and keeps the Chart Editor open.
• Cancel Cancel the current editing session and close the Chart Editor
• Apply Save the current record settings, draw the chart, and keep the Chart Editor open

File identification

The importer operates on files with the extension .fcs and .lmd

Configuration Options

The FCS Importer does not provide any import configuration properties.

Limitations and Known Issues

• The importer currently works only on local files.
• Files without extension .fcs or .lmd cannot presently be imported into Catalyzer as FCS files.
• Changing the FCS Histogram and FCS Dotplot classes causes the Chart Editor to fail when attempting to save charts.