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# <img src = './images/fcsrunner_icon.png'> FcsRunner
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VBA tool to perform imaging and fluorescence correlation spectroscopy measurements (FCS) and automatically save FCS positions to xml file. To be used with Zeiss LSM microscopes running with ZEN black.
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VBA tool to perform imaging and fluorescence (cross)correlation spectroscopy measurements (F(C)CS) and automatically save FCS positions to xml file. To be used with Zeiss LSM microscopes running with ZEN black (version >= 2010). The tool can be used to create data for FCS-calibrated imaging.
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FCS measurements are performed at multiple stage positions. Typically one stage position per cell. At each stage position the user specifies FCS points. After all positions have been specified the users starts the acquisition. Then for each position an image is acquired and FCS measurements are performed. The image and FCS settings are given by the current settings in ZEN.
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For each stage position user can specify different FCS points. Each position will be visited and imaging and FCS executed. Only one imaging and FCS settings can be used at once.
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<a name=back></a>
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... | ... | @@ -14,22 +15,26 @@ For each stage position user can specify different FCS points. Each position wil |
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> **Disclaimer:**
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> FcsRunner has been tested on Zeiss LSM 780 microscopes with ZEN 2010, 2011, and 2012, and LSM880 microscopes with ZEN2.1 and ZEN2.3. We don’t guarantee that it will work on other configurations and we don’t take any responsibility for damage occuring during or after use of FcsRunner.
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> FcsRunner has been tested on Zeiss LSM 780 microscopes with ZEN 2010, 2011, and 2012, and LSM880 microscopes with ZEN2.1 and ZEN2.3. We don’t guarantee that it will work on other configurations and we don’t take any responsibility for damage occurring during or after use of FcsRunner.
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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. ./images
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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 | |
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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/assignMacro.PNG" width = "400px"> | 4. Provide a *Menu Entry*, a text, and select *fcs\_runner.lvb* as project. This will make the macro available in the menu.
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### Save *.raw data
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The compute corrected correlation functions from the photon counts some programs require the raw data. In ZEN you need to specify this in the *Maintain* menu. A directory does not need to be specified. FCSRunner copies the **.raw* files in the current directory.
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<p align = 'center'> <img src="./images/rawcounts.PNG" width = "200px"> </p>
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### Trouble shooting the installation
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For any issues please contact one of the developers in the Ellenberg group at EMBL, Heidelberg. For errors that appear in the ErrorLog window please provide the PipelineConstructor.err file and the full version of your ZEN software (Help->About). If you have a ZEN version higher than 2010 and the macro complains that it does not find ```Zeiss.Micro.AIM.ApplicationInterface.dll```, you may need to register it manually.
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