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## [<img src="./images/up.PNG">](#back) <a name="installation"></a> Installation and start
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## [<img src="./images/up.png">](#back) <a name="installation"></a> Installation and start
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* Copy the file *fcs_runner.lvb* (for ZEN2010 use the file *fcs\_runner\_ZEN2010.lvb* instead) and the directory *resources* to a directory that can be accessed from the computer running ZEN.
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* In ZEN open the *Macro* tab (*Alt-F8*), click on *Edit Macro*.
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|Load the macro into ZEN | Explanations of the buttons |
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|:--------------|:---------------------------- |
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| <img src="./images/loadMacro.PNG" width = "400px"> | 1. Load the macro. Browse to the file *fcs\_runner.lvb* <br /> or *fcs\_runner\_ZEN2010.lvb* for older ZEN versions. <br /> 2. Run the macro. <br /> 3. To insert the macro in your list of macros click on the tab.|
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| <img src="./images/assignMacro.PNG" width = "400px"> | 4. Provide a *Menu Entry*, a text, and select *fcs\_runner.lvb* as project. |
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| <img src="./images/loadMacro.png" width = "400px"> | 1. Load the macro. Browse to the file *fcs\_runner.lvb* <br /> or *fcs\_runner\_ZEN2010.lvb* for older ZEN versions. <br /> 2. Run the macro. <br /> 3. To insert the macro in your list of macros click on the tab.|
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| <img src="./images/assignMacro.png" width = "400px"> | 4. Provide a *Menu Entry*, a text, and select *fcs\_runner.lvb* as project. |
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### Save *.raw data
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... | ... | @@ -58,7 +58,7 @@ C:\Windows\Microsoft.NET\Framework\v4.0.30319\RegAsm.exe /tlb /codebase Zeiss.Mi |
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<a name="sectionTwo"></a>
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## [<img src="./images/up.PNG">](#back) <a name=experiment></a>Running an experiment
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## [<img src="./images/up.png">](#back) <a name=experiment></a>Running an experiment
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Before running an experiment the user first defines imaging and FCS settings in ZEN. The macro will use these settings. When pressing one of the running options; the macro will acquire an image and perform the FCS measurements. In additon, a [xml file](#xmlfile) is generated that contains the image coordinates.
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> **Imaging Settings** For FCS-calibrated imaging use an uneven number of Z slices (1, 3, 5, ...). This ensures that each FCS measurement corresponds to a pixel in the image.
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> **BUG** When several stage positions are added some positions may end up shifted with respect to the expected location. Therefore, before launching the measurements do visit all stage positions (double click) and verify the correct positioning. Eventually update the position of a wrongly assigned stage position.
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<p align = 'center'><img src="./images/fcsRunner.PNG" width = "400px"></p>
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<p align = 'center'><img src="./images/fcsRunner.png" width = "400px"></p>
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1. Specify the number and location/type of `FCS points per object`
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2. In the **FCS Positions** frame the user can `Add` FCS points to the current stage position. The other buttons will `Remove` a highlighted point or `Remove All` FCS points
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<a name="sectionThree"></a>
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## [<img src="./images/up.PNG">](#back) <a name="fileoutput"></a> File output
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## [<img src="./images/up.png">](#back) <a name="fileoutput"></a> File output
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FCS Runner generates the following files:
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* `ID_baseFileName.czi|lsm`: Image file associated to FCS measurement
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