... | ... | @@ -281,8 +281,7 @@ Specifies stage positions. Coordinates with respect to upper left corner of the |
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`X1;X2;X3;...` | X positions with respect to left corner in pixels
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`Y1;Y2;Y3;...` | Y positions with respect to upper corner in pixels
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`Z1;Z2;Z3;...` | Z positions with respect to bottom slice in pixels
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`Z1;Z2;Z3;...` | Z positions with respect to bottom slice in pixels. If this key is left empty current focus position is used.
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####Keys **fcsX**, **fcsY**, **fcsZ**
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... | ... | @@ -293,7 +292,7 @@ Specifies FCS scanner positions. Coordinates with respect to upper left corner o |
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----------- | ------
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`X1;X2;X3;...` | X positions with respect to left corner in pixels
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`Y1;Y2;Y3;...` | Y positions with respect to upper corner in pixels
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`Z1;Z2;Z3;...` | Z positions with respect to bottom slice in pixels
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`Z1;Z2;Z3;...` | Z positions with respect to bottom slice in pixels. If this key is left empty current focus position is used.
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<a name="rois"></a>
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... | ... | @@ -314,4 +313,33 @@ For an ellipse specify 3 points: the center of the ellipse and a point on axis1 |
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## <a name= trigger></a> Trigger1 and Trigger2 pipelines
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The pipelines Trigger1/2 are only executed when the command trigger1 or trigger2 is received through the windows registry. |
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The pipelines **Trigger1/2** are only executed when the command ```trigger1``` or ```trigger2``` is received through the windows registry [**CodeMic**](#codemic). A typical workflow is a multi-position low-resolution imaging using the **Default** pipeline. When objects of interest are detected using online image analysis then the **Trigger1/2** pipeline is started with position(s) specified using the registry keys [XYZ](#xyz). Several imaging/stage positions can be passed to the macro simultaneously, these will be imaged one after the other.
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Multiple imaging positions can also be specified sequentially. In this case the **Trigger1/2** pipelines start when stage positions are specified within a time interval or when a maximal number of positions has been reached. If no XYZ coordinates are specified then imaging is performed at the current stage and focus position of the **Default** pipeline. When all repetitions of all positions are finished the imaging continues with the **Default** pipeline. The setup of the pipelines is similar as for the default pipeline. Within a **Trigger1/2** pipeline additional online image analysis steps can be specified.
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Trigger1/2 | Explanations of the buttons
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-----------------|----------------------------
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<img src="./images/PipCon_trigger1.PNG" width = "400px"> | 1. Specify order of tasks as for Default pipeline <br/> 2. Specify whether to further process some of the imaging jobs <br/> 3. Specify repetitions <br/> 4. Start pipeline after one position has been specified and **max. waiting (sec)** interval has elapsed<br/> 5. Start pipeline when at least **max # Pts** stage positions have been specified. <br/> 6. If **Keep parent position** is unchecked then the stage position of the **Default** pipeline from which the trigger has been released is deleted. This option is useful to avoid triggering repeated false positives from the same position.
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# Example workflows with MyPiC
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Here we provide examples of workflows that can be performed using MyPiC. The strength of the tool is in combination with the communication of an image analysis tool. Here we use an imageJ based tool that can be obtained from ....
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## Without adaptive feedback
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### Reflection based Autofocus and imaging
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### Intensity center of mass based tracking
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## Using adaptive feedback
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### Object based tracking in 4D
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### Adaptive feedback rare event detection
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### Adaptive feedback automated FC(C)S of single cells
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### Object based tracking in 4D and FC(C)S
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### Automated fluorescence recovery after photobleaching experiments |
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