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Add workflow containers to "Ephys Synchronization" tutorial #133

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Add workflow containers to "Ephys Synchronization" tutorial #133

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12 changes: 12 additions & 0 deletions tutorials/synching-ephys.md
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,10 @@ The general approach when synchronizing two independent data acquisition clocks

### **Exercise 1:** Synchronizing behaviour events with ephys

:::workflow
![Syncing ephys with behavior](~/workflows/syncing-ephys-behavior.bonsai)
:::

- Insert a `KeyDown` source.
- Insert an `Equal` transform and set its `Value` to one of the keys. The output of this operator will toggle between `True` and `False` depending on whether the key press matches the specified key.
- Insert a `DigitalOutput` sink and connect it to Arduino pin 13.
Expand All @@ -22,6 +26,10 @@ The general approach when synchronizing two independent data acquisition clocks

### **Exercise 2:** Synchronizing video with ephys using an LED

:::workflow
![Syncing ephys with video](~/workflows/syncing-ephys-video.bonsai)
:::

- Using the workflow from the previous exercise, insert a `CameraCapture` source and point the camera such that you can see clearly both the LED and the computer keyboard.
- Insert a `VideoWriter` sink and configure the `FileName` with a path ending in `.avi`.
- Insert a `Crop` transform and set the `RegionOfInterest` property to a small area around the LED.
Expand Down Expand Up @@ -53,6 +61,10 @@ However, you can take advantage of the fact that all pixels in a frame are prese

In this exercise you will track the display of a very simple visual stimulus: a transition between black and white.

:::workflow
![Syncing ephys with visual stimulus](~/workflows/syncing-ephys-visual.bonsai)
:::

- Insert a `SolidColor` source and set its `Size` property to a positive value, e.g. 100,100.
- Insert a `Timer` source and set the `Period` to one second.
- Insert a `Mod` transform and set its `Value` property to 2.
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79 changes: 79 additions & 0 deletions workflows/syncing-ephys-behavior.bonsai
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<?xml version="1.0" encoding="utf-8"?>
<WorkflowBuilder Version="2.8.5"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xmlns:ard="clr-namespace:Bonsai.Arduino;assembly=Bonsai.Arduino"
xmlns:wie="clr-namespace:Bonsai.Windows.Input;assembly=Bonsai.Windows.Input"
xmlns:p1="clr-namespace:System.Windows.Forms;assembly=System.Windows.Forms, Version=4.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089"
xmlns:eph="clr-namespace:Bonsai.Ephys;assembly=Bonsai.Ephys"
xmlns:dsp="clr-namespace:Bonsai.Dsp;assembly=Bonsai.Dsp"
xmlns="https://bonsai-rx.org/2018/workflow">
<Workflow>
<Nodes>
<Expression xsi:type="Combinator">
<Combinator xsi:type="ard:CreateArduino">
<ard:Name>Arduino</ard:Name>
<ard:PortName>COM1</ard:PortName>
<ard:BaudRate>57600</ard:BaudRate>
<ard:SamplingInterval>19</ard:SamplingInterval>
</Combinator>
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="wie:KeyDown">
<wie:Filter>Space</wie:Filter>
<wie:SuppressRepetitions>false</wie:SuppressRepetitions>
</Combinator>
</Expression>
<Expression xsi:type="Equal">
<Operand xsi:type="WorkflowProperty" TypeArguments="p1:Keys">
<Value>Space</Value>
</Operand>
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="ard:DigitalOutput">
<ard:PortName>Arduino</ard:PortName>
<ard:Pin>13</ard:Pin>
</Combinator>
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="eph:Rhd2000EvalBoard">
<eph:BitFileName>main.bit</eph:BitFileName>
<eph:SampleRate>SampleRate20000Hz</eph:SampleRate>
<eph:ExternalFastSettleEnabled>false</eph:ExternalFastSettleEnabled>
<eph:LowerBandwidth>0.1</eph:LowerBandwidth>
<eph:UpperBandwidth>7500</eph:UpperBandwidth>
<eph:DspCutoffFrequency>1</eph:DspCutoffFrequency>
<eph:DspEnabled>true</eph:DspEnabled>
<eph:CableDelayA xsi:nil="true" />
<eph:CableDelayB xsi:nil="true" />
<eph:CableDelayC xsi:nil="true" />
<eph:CableDelayD xsi:nil="true" />
</Combinator>
</Expression>
<Expression xsi:type="MemberSelector">
<Selector>BoardAdcData</Selector>
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="dsp:SelectChannels">
<dsp:Channels>
<dsp:int>0</dsp:int>
</dsp:Channels>
</Combinator>
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="dsp:MatrixWriter">
<dsp:Path>test.bin</dsp:Path>
<dsp:Suffix>None</dsp:Suffix>
<dsp:Overwrite>false</dsp:Overwrite>
<dsp:Layout>ColumnMajor</dsp:Layout>
</Combinator>
</Expression>
</Nodes>
<Edges>
<Edge From="1" To="2" Label="Source1" />
<Edge From="2" To="3" Label="Source1" />
<Edge From="4" To="5" Label="Source1" />
<Edge From="5" To="6" Label="Source1" />
<Edge From="6" To="7" Label="Source1" />
</Edges>
</Workflow>
</WorkflowBuilder>
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