In the box to the right, you can type the names of selected parameters to always display as linear (for example, when doing Cell Cycle analysis, In the upper-most area, you can select which parameters should be shown with logarithmic scaling by default.
on the Workspace tab you will see Reading DiVa and other 32 bit Data Files. To change these Preferences, go to the menu FlowJo > Preferences. In log and both side scatter and forward scatter in linear format.
Since data exported from the BD FACSDiVaT software (except FCS 2 files) is saved in linear format, the user must tell FlowJo in which format to display the data (log or linear.) The factory default FlowJo Preference is to show all fluorescence parameters To edit the Acquisition matrix, you must first createĪ new matrix that is a copy of the acquisition matrix, and then edit that. In order to replace the previous matrix, simply apply the new one to the data file. The Acquisition matrix can be edited or an entirely new matrix can be created and applied to the data files. The option key and click on the graph window axis pulldown lists and choose parameters without brackets To look at the parameters uncompensated, hold Therefore, when you add the data files to a FlowJo workspace, they show up with a red bar beside them (indicating they have been compensated). Is referred to as the Acquisition matrix).įlowJo will apply the Acquisition matrix to the data files. If the data was compensated during acquisition, this compensation matrix is included in the data file (in FlowJo, it Import to FlowJoĪll data exported from the BD FACSDiVaT software (except FCS 2 files) is saved in linear, uncompensated format.
FCS 3.0 data files from BD FACSDivaT Software v4.0 are in floating-point format and are fully annotated.
BD recommends that you upgrade to version 4.0, and has indicated that this is a free upgrade.īD FACS DiVaT version 4: - Export as FCS 3.0.
Uncompensated data will not be transformed (but compensated will be). Then export as FCS 3.0, 18 bit resolution (262,144 channels). It is just when the users want to adjust quadgate in flowjo, they need to move the gate four times instead of one.BD FACS DiVaT version 4.01: - export as Experiment - This format allows for the best transformed displays of uncompensated parameters however, very little annotation (stain names, acquisition time, etc) is included in the file. This issue does not affect any correctness of the results (e.g.
I used FlowJo 10.2 Windows for the tests above. Note that here I need to change the format for all the four rectangular gates to make it work. I manually changed the rectangular gate in CytoML export file to the flowjo format, and then flowjo can render it as a quadgate. Therefore, opening it in flowjo render quadgate as 4 rectangular gates. The export from CytoML saves rectangular gate from both cases in the same way. For the example above, it refers to PE+FITC- region.
The later one only specifies the center point of the quandrant, and refers to min and max to decide which quad is this rectangle. In FlowJo, there is an implicit difference between the typical rectangular gate and rectangular gates rendered from quadgate There is no such concept as quadgate in GatingSet as well as flowjo workspace, they are both stored as 4 rectangular gates. I did some experiments yesterday and here is what I found: Yes, I am sure I am looking at the same population node. Quadrant gate in CytoML (difference highlighted):Ĭould this be improved? I am not sure whether this is more related to flowWorkspace or flowCore I compared the xml specification between CytoML and FlowJo: After export gating set to flowjo workspace GatingSet2flowJo, the quadrant gate is parsed by FlowJo as four independent rectangular gates.