flyPAD software

We have designed flyPAD acquisition software to work inside the Bonsai environment.

Bonsai image

Bonsai is open-source software for processing streams of data, developed by Gonçalo Lopes at the Champalimaud Centre for the Unknown. It can be used for analyzing videos in real time, controlling behavioral experiments, or acquiring data from the flyPAD. With BONSAI you tell your computer what to do not through long listings of text but by manipulating graphical elements in a workflow. Workflow elements in BONSAI represent asynchronous streams of data which can be connected together to perform complex operations.
  • Developed entirely in C#
  • Easy to extend with your own modules. There is no need to learn yet another API as BONSAI uses entirely Rx under the hood
  • Number of simultaneous operations limited only by your system and hardware
  • Intuitive and easy to understand interface
  • Various algorithms for image and digital signal processing included
  • Each processing step can be independently visualized while the workflow is running

How to make setup Bonsai on your computer

First you need to Download the latest version of Bonsai. Run Bonsai, then go to 'Tools'=>'Manage Packages'. We recommend installing all packages. FlyPAD package is one of them. You need to connect the flyPAD to a computer to any available USB2.0 port (it may not work with blue USB 3.0 ports). screenshot1 on the left side of the bonsai window you will see a list of all the Installed Bonsai modules. Go to 'Source'=>'FlyPad'=>'FlyPadSourse' and drag it onto the main Bonsai window. screenshot
Click on the 'FlyPad Icon' (F) with the left mouse button and Select available 'LocationID' from the menu on the right. If no port is available check that the flyPAD is connected to the computer and whether the FTDI drivers are installed.
Then select 'Sink'=>'Dsp'=>'MatrixWriter' and again drag it to the workspace, but now drop it on the FlyPadSource module. You can check the available options and properties for each node after you LeftClick on top of the icon. Lets click on the 'M' icon and change the 'Layout' to 'RowMajor'. We will need it later when we would import the recorded data into Matlab. screenshot
In the 'Path' section select the folder and the filename where you want to save the file. You can automatically append a Timestamp or number to the file by choosing an appropriate entry in the 'Suffix'

flyPAD filename convention

If you are planning to use my Matlab script to process the data you should follow my naming convention: filename has a certain structure to it, and the code is using the filename to assign conditions to different channels for example the file:
starts with "CapacitanceData"(case sensitive)
followed by "_C01_01_24_C02_25_44_C03_45_64" This is an identifier for various conditions in this example there are 3 conditions: C01, C02,C03
Condition 1(C01) is located on channels 01-24;
Condition 2(C02)on channels 25-44 and
Condition 3(C03) on channels 45-64.
Note there are 64 channels in total, each arena has 2 channels.
2014-02-21T11_07_11 is an automatically generated Timestamp suffix

Starting the recording

Now you need to put the solutions you want to test on the electrodes, load the flies in the chambers, then select 'Workflow'=>'Start' or press 'F5'.
Whenever the experiment is over press 'Workflow'=>'Stop' or stop.

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