This option displays the name as it is on the system disk (i.e. To avoid this problem, choose the next option, Use Data File Name. NOTE: Options chosen when acquiring your data can cause all the samples in the workspace to be named identically (i.e., each file name is missing the suffix. When you choose to display the sample's file name from the Sample Name Keyword - FlowJo examines the FCS keyword header informationĪnd uses the sample name keyword from the data file as the file name in the workspace. Just below, you can choose how FlowJo will display the data file names in the workspace window list. When FlowJo opens, it opens a new workspace window as well. Unchecked, the number will reflect the portion of all cells in the Of Parent allows you to specify that the percentage shown in the Statistic column of the workspace refers to the portion of the immediate parent population. Further options let you choose to have FlowJo display a light grid over the sampleĪnd group list to aid in visualization.� The setting Gate Statistic is Freq. The time counter is shown in the tool bar of the workspace window. Time Since Last Save to show the amount of time that has past since you saved this workspace. Please note that if you change the parameter scale or transformation settings, this will take effect in a new workspace.The section marked Appearance defines preferences about the how the workspace appears. Setting these preferences is only required once. The fcs files will always use the cytometer settings for whichever cytometer was used to generate the files. Note: There is not way to “select” which Cytometer an fcs file will use. Select any of the options on the left and use the options presented to alter the way in which the data is displayed by default in FlowJo v10. For example, if Attune data has never been loaded into your copy of FlowJo, you will not see this as an option. These sets are only populated when a data file of a particular data type are loaded.
Click on any of them to view the default scaling sets. The list on the left provides all the default cytometers. If these default setting do not scale the data properly for your application, please let us know to use Cytometer PreferencesĬlick on the preferences and choose Cytometers. FlowJo is designed with scaling settings for each cytometer, based on our understanding of the acquisition software, and the way the file is written. If the default scaling preferences are not exactly correct for your data, the values can be manipulated to scale the data exactly as displayed on the instrument during acquisition. They can then load data acquired on a Beckman Coulter Cyan and have it scaled a different way.įurthermore, with the new cytometer scaling preferences, the user can manipulate the preference sets for each cytometer. This way, a user can load data acquired on a BD instrument running FACSDiva and have it scaled one way (similar to FACSDiva). In addition, a preference set is generated for the data from all the different cytometers that have been opened in FlowJo. Default scaling preferences are then loaded into the preference pane based on the value of the $CYT keyword.
In version 10, the cytometer preferences are set by reading the cytometer ($CYT) keyword from the files upon load. Hence, scaling did not automatically change based on the cytometer from which the data were acquired. In older versions of FlowJo, the scaling was limited to number of decades and general transform settings globally.
FLOWJO REFERENCE SOFTWARE
Hence, the software can control the scaling and transformation upon load. All FCS 3.1 data is written as linear, untransformed and uncompensated data. However, with FCS 3.1, the digital standard, scaling and display of data is controlled by the software in which it is analyzed. FCS 2.0 data is considered the analog standard and scaling is controlled by the file. However, these can be changed or refined. For more information about FlowJo’s display of data for specific cytometers, please see FlowJo and Your Cytometer.ĭata is written in two common standards, FCS 2.0 and FCS 3.1 (previously FCS 3.0, Data File Standard for Flow Cytometry, Version FCS 3.1, Normative Reference).
We have a number of default settings for the various cytometers set. FlowJo version 10 allows you to set up scaling preferences based on the specific cytometer being used.
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