Flowing Sotware documentation

Flowing Software does not have a written manual. Instead, everything is packed in a screen capture video, which shows everything you need for a successful analysis.

Contents of the video:

  1. Basic usage (0:04)
  2. Regions (2:24)
  3. Connections (4:42)
  4. Definitions (7:07)
  5. Collection tools (8:26)
  6. Overlay Histogram (13:43)
  7. Automation (14:43)
  8. Manipulation tools (19:19)
  9. Calculation tools (22:11)

Here you can find the screen capture videos for each tool.

Dot plot
Statistics view
Statlist view

Metadata viewer
Image collector
Intensity plots
Folder runner
Overlay histograms

Forward jumper
Change parameter names
Event number reducer
Lin-Log changer

Ratio calculator
Virtual gain
Update in column
Update then the name contains something
Update counter

Cell calculator
Collector list

Supported file types
Flowing Software reads standard flow cytometry format (FCS), both FCS2.0 and FCS3.0.
However, although the format should be standard, manufacturers write it slightly differently. Therefore there is a risk that the software is not able to read all files.

TXT files
If you have some other kind of statistical data, and you would use the visualization and analysis methods Flowing Software offers, it is possible. From top menu select File – Open TXT File…
Prepare your data like this:

1) Open it with e.g. MS Excel
2) Add some keywords into the beginning of the data: name, max, display, scalemin and scalemax.
3) Save as “Text (tab delimited) (*.txt)”
4) Open with Flowing Software.

The screenshot below shows the example, how the data would look like before the saving.

Description of the keywords:

Name: The parameter name. This parameter is obligatory.
Max: Defines the maximum value of the scale. This parameter is obligatory.
Min: Defines the minimum value. This doesn’t have any effect without scalemin and scalemax. This parameter is optional.
Display: [lin / log] Defines whether the data is visualized as linear or logarithmic. Note! This doesn’t have any effect to the statistics, it affects only the visualization. This parameter is optional. If no value, default is linear.
ScaleMin: Defines the new minimum value for the parameter. This parameter is optional.
ScaleMax: Defines the new maximum value for the parameter. This parameter is optional.

Example for using scaling:

You have the data, having values from -20 to 20. Because Flowing Software is not meant for visualizing negative values, you would like to scale the data from 0 to 100. In this case, give the following values:

Flowing Software calculates the scaling when loading the data.

Analysis files
You can save your analysis from File – Save Analysis. The resulting file is a .flow file.
The analysis file contains tools, gates, connections and the information, which data file is loaded into the tools. However, it doesn’t contain the data itself, only the reference.

If you move the data files from one place to another, it is possible that when you open the analysis file, it will warn you that the data files can’t be found. However, the software loads the analysis (it just replaces the missing files with generic data files), so you can reload the data from new location to the tools.

Portable Analysis Files
You can choose ‘Save as Portable…’ which makes it easier to copy the analysis to another computer.
When you save the analysis as portable, the data file will contain only the file names, but not path. Then you can copy the analysis and necessary data files into one folder and pack it with e.g. ZIP. Now the analysis file is ready for sending to the collaborator.

When the collaborator opens the package, she is able to open the file without problems, as long as the data files are in the same folder as the analysis file.