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... | @@ -60,28 +60,13 @@ Throughout this manual we will use following naming definitions |
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* Copy the file *PipelineConstructor.lvb* (for ZEN2010 use the file *PipelineConstructor\_ZEN2010.lvb*) and the directory *resources* to a directory that can be accessed from the computer running ZEN.
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* Copy the file *PipelineConstructor.lvb* (for ZEN2010 use the file *PipelineConstructor\_ZEN2010.lvb*) 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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* In ZEN Open the *Macro* tab (*Alt-F8*), click on *Edit Macro*.
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<style="width:99%"> Load the macro into ZEN| Explanations of the buttons
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Load the macro into ZEN| Explanations of the buttons
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<img src="./images/loadMacro.PNG" width = "400px"> | 1. Load the macro. Browse to the file *PipelineConstructor.lvb* <br /> or *PipelineConstructor\_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/loadMacro.PNG" width = "400px"> | 1. Load the macro. Browse to the file *PipelineConstructor.lvb* <br /> or *PipelineConstructor\_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"> | provide a *Menu Entry*, a text, and select *PipelineConstructor.lvb* as project.
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<img src="./images/assignMacro.PNG" width = "400px"> | provide a *Menu Entry*, a text, and select *PipelineConstructor.lvb* as project.
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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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You can try this to fix
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• Open a console window (cmd.exe)
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• Go to the ZEN path: ``cd ..\..\ZEN``
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• Register the ```Zeiss.Micro.AIM.ApplicationInterface.dll```
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``` C:\Windows\Microsoft.NET\Framework\v4.0.30319\RegAsm.exe /tlb /codebase Zeiss.Micro.AIM.ApplicationInterface.dll ```
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• When you uninstall ZEN, make sure to un-register
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```C:\Windows\Microsoft.NET\Framework\v4.0.30319\RegAsm.exe/u /tlb /codebase Zeiss.Micro.AIM.ApplicationInterface.dll```
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# <a name="back"></a> Setting up an experiment with MyPiC
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# <a name="back"></a> Setting up an experiment with MyPiC
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... | @@ -322,11 +307,13 @@ Trigger1/2 | Explanations of the buttons |
... | @@ -322,11 +307,13 @@ Trigger1/2 | Explanations of the buttons |
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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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<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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# Example imaging 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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Workflows without adaptive feedback do not require any further program.
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## Without adaptive feedback
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## Without adaptive feedback
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### Reflection based Autofocus and imaging
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### Reflection based Autofocus and imaging
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Define
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### Intensity center of mass based tracking
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### Intensity center of mass based tracking
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... | | ... | |