Flowing Software

Documentation

At the moment Flowing Software does not have any written manual. Instead, everything is packed to the screen capture video, which shows everything you need for succesful analysis.

Tutorial Video for Flowing Software version 2 (in Youtube)

You can also download the video here (.wmv)

Content 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)

Tool Specific Help

Here you can find the screen capture videos for each tool. The videos are couple of minutes long.

You can find the same videos from Flowing Software by selecting one tool and choosing from top menu Help - Help for Selected Tool.

Dot plot
Histogram
Intensity Plot
Overlay Histogram
Meta Data Viewer

Statistics
StatList
Token
Image Collector
Collector List

Folder Runner
Forward Jumper
Update Counter
Update in Column
Update when the name contains...

Parameter name changer
Lin/Log Changer
Event number reducer
Post Compensation
Virtual Gain

Calculate Ratio of Two Parameters
Statistics Calculator
Advanced Cell Calculator

Supported file types

Flowing Software reads standard flow cytometry format (FCS), both FCS2.0 and FCS3.0.

However, although the format should be standard, all manufacturers write it slightly differently. Therefore there is a risk that the software is not able to read all files.

We have recieved the single data files created with other instruments, and according to those files, Flowing Software reading routine should read those files with no problem. However, it is not guaranteed that all file types can be opened.

Read 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 oblicatory.
Max: Defines the maximum value of the scale. This parameter is oblicatory.
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, you would like to scale the data from 0 to 100. In this case, give the following values:
Min:-20
Max:20
ScaleMin:0
ScaleMax:100

Flowing Software calculates the scaling when loading the data.

Analysis files

You can save your analysis from File - Save Analysis. The resulting file is .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's 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/he is able to open the file without problems, as long as the data files are in the same folder as the analysis file.