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* **Pipeline**<a name = "pipeline"></a>: A concatenation of imaging and/or FCS jobs that will be executed one of the other. In MyPiC we have a Default pipeline that is executed at every position and 2 pipelines that can be triggered with external commands (Trigger1 and Trigger2).
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## Installation
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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. In ZEN Open the *Macro* tab (*Alt-F8*), *Edit Macro* and click (1)*Load* in the *Macro Control* window. Browse to the file *AutofocusScreen\_ZEN.lvb*. Click on (2)*Run*. To insert the macro in your list of macros click on (3)*Assign Macro* provide a *Menu Entry*, a text, and select *AutofocusScreen\_ZEN.lvb* as project.
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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. 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="400"> | 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="400"> | provide a *Menu Entry*, a text, and select *PipelineConstructor.lvb* as project.
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![loadMacro.PNG](./images/loadMacro.PNG "load" "width:450px;display:block; margin-left:auto; margin-right:auto")
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![assignMacro.PNG](./images/assignMacro.PNG "assign" "width:450px;display:block; margin-left:auto; margin-right:auto")
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### Trouble shooting for the installation:
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For any issues please contact one of the developers (at the moment Antonio Politi,
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7. [Define additional pipelines to be triggered](#trigger)
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8. [Reloading settings](#reload)
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### <a name=jobsetterimaging></a> JobSetter for imaging jobs
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The jobSetter is started by clicking on the corresponding button (1) *JobSetter*
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![jobsettercall](./images/PipCon_upperpart.PNG "grid" "width:50px")
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This will open a window
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![jobsettercall](./images/jobsetter.PNG)
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This wiki uses the [Markdown](http://daringfireball.net/projects/markdown/) syntax.
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The wiki itself is actually a git repository, which means you can clone it, edit it locally/offline, add images or any other file type, and push it back to us. It will be live immediately.
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Go ahead and try:
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```
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$ git clone https://micronaut@bitbucket.org/micronaut/mypic.git/wiki
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```
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Wiki pages are normal files, with the .md extension. You can edit them locally, as well as creating new ones.
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## Syntax highlighting
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You can also highlight snippets of text (we use the excellent [Pygments][] library).
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[Pygments]: http://pygments.org/
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Here's an example of some Python code:
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### [<img src="./images/up.PNG">](#back) <a name=jobsetterimaging></a> JobSetter for imaging jobs
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The **JobSetter** is started by clicking on the corresponding button (1) *JobSetter*
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```
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#!python
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def wiki_rocks(text):
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formatter = lambda t: "funky"+t
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return formatter(text)
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```
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<img src="./images/PipCon_upperpart.PNG" width="500">
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In the JobSetter window the user can create several [imaging jobs](#imagingjob) to be used in the [pipelines](#pipeline). The user first set imaging settings in ZEN and then upload them to the VBA macro either by creating a new job or updating it. Jobs can also be created by loading a set of microscopy images (.czi or .lsm) previously acquired on the same microscope.
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> **Caution** Loading setting from images acquired on a different microscope may not work and may impair/harm the system.
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You can check out the source of this page to see how that's done, and make sure to bookmark [the vast library of Pygment lexers][lexers], we accept the 'short name' or the 'mimetype' of anything in there.
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[lexers]: http://pygments.org/docs/lexers/
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JobSetter window | Explanations of the buttons
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-------| -------------
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<img src="./images/jobSetter.PNG" width="500">| 1. Create a new job with current imaging settings. <br /> 2. Load imaging jobs from saved images (.czi or .lsm). <br/> 3. Change name of current job (highlighted job). <br/> 4. Acquire all or one jobs and save images to a file. <br/> 5. Remove a job from the list. <br/> 6. Update current job with settings in ZEN. <br/> 7. Load settings of current job into ZEN. <br/> 8. Stop acquisition. <br/> 9. Acquire current job. <br/> 10. List of available jobs. <br/> 11. Short description of current job. <br/> 12. Available tracks for current job.
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### [<img src="./images/up.PNG">](#back)<a name=jobsetterimaging></a> JobSetter for FCS jobs
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Have fun! |