|
|
# Welcome
|
|
|
<style>
|
|
|
p
|
|
|
{
|
|
|
width:800px;
|
|
|
word-wrap:break-word;
|
|
|
}
|
|
|
li
|
|
|
{
|
|
|
width:800px;
|
|
|
word-wrap:break-word;
|
|
|
}
|
|
|
|
|
|
Welcome to your wiki! This is the default page we've installed for your convenience. Go ahead and edit it.
|
|
|
table {
|
|
|
border-collapse: collapse;
|
|
|
width:800px;
|
|
|
}
|
|
|
td {
|
|
|
padding: 0;
|
|
|
}
|
|
|
</style>
|
|
|
# Microscopy Pipeline Constructor (MyPiC)
|
|
|
|
|
|
## Wiki features
|
|
|
MyPiC is a Visual Basic for Application (VBA) macro to be used with Zeiss confocal microscopes running with the ZEN software (version black).
|
|
|
The macro allows
|
|
|
|
|
|
* Autofocus based on reflection and fluorescence multi-location time series
|
|
|
* Fluorescence based “Object” Tracking
|
|
|
* Multi-location time-lapse experiments
|
|
|
* Flexible combination of several independent Z-stack and channel settings
|
|
|
* Flexible combination of several fluorescence correlation spectroscopy (FCS) measurements settings
|
|
|
* [Adaptive Feedback microscopy support of two triggable imaging and FCS workflows](#adaptiveFeedback)
|
|
|
|
|
|
|
|
|
|
|
|
> **Disclaimer:**
|
|
|
> MyPiC for ZEN has been extensively 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 MyPiC.
|
|
|
|
|
|
## Definitions
|
|
|
Throughout this manual we will use following naming conventions:
|
|
|
|
|
|
* **Imaging job**<a name = "imagingjob"></a>: Contains settings used for imaging. They are defined by laser used, Z-stack, pixel-dwell time etc. Basically anything you can define in the ZEN software.
|
|
|
* **FCS job**<a name = "fcsjob"></a>: Contains settings used for FCS
|
|
|
* **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).
|
|
|
|
|
|
## Installation
|
|
|
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.
|
|
|
|
|
|
![loadMacro.PNG](./images/loadMacro.PNG "load" "width:450px;display:block; margin-left:auto; margin-right:auto")
|
|
|
![assignMacro.PNG](./images/assignMacro.PNG "assign" "width:450px;display:block; margin-left:auto; margin-right:auto")
|
|
|
|
|
|
### Trouble shooting for the installation:
|
|
|
For any issues please contact one of the developers (at the moment Antonio Politi,
|
|
|
politi@embl.de or the Ellenberg lab at EMBL).
|
|
|
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 >
|
|
|
2010 (or > 2.1) and the macro complains that it does not find Zeiss.Micro.AIM.ApplicationInterface.dll, you may need to register it manually.
|
|
|
You can try this to fix
|
|
|
|
|
|
• Open a console window (cmd.exe)
|
|
|
|
|
|
• Go to the ZEN path: “cd ..\..\ZEN
|
|
|
|
|
|
• Register the Zeiss.Micro.AIM.ApplicationInterface.dll
|
|
|
|
|
|
> C:\Windows\Microsoft.NET\Framework\v4.0.30319\RegAsm.exe /tlb /codebase Zeiss.Micro.AIM.ApplicationInterface.
|
|
|
dll
|
|
|
|
|
|
• When you uninstall ZEN, make sure to un-register
|
|
|
|
|
|
>C:\Windows\Microsoft.NET\Framework\v4.0.30319\RegAsm.exe/u /tlb /codebase Zeiss.Micro.AIM.ApplicationInterfa
|
|
|
|
|
|
|
|
|
## <a name="back"></a> Setting up an experiment with MyPiC
|
|
|
|
|
|
After the PipelineConstructor has started the user needs to proceed through several steps before starting an experiment
|
|
|
|
|
|
1. [Define one or several imaging jobs using the jobSetter](#jobsetterimaging)
|
|
|
2. [Define one or several imaging jobs using the jobSetter (optional)](#jobsetterfcs)
|
|
|
3. [Add jobs to the Default pipeline](#default)
|
|
|
4. [Define the number of repetitions and repetition interval for the default pipeline](#repetitions)
|
|
|
5. [Define stage positions and/or a grid](#positions)
|
|
|
6. [Define the directory where to save the images](#saving)
|
|
|
7. [Define additional pipelines to be triggered](#trigger)
|
|
|
8. [Reloading settings](#reload)
|
|
|
|
|
|
### <a name=jobsetterimaging></a> JobSetter for imaging jobs
|
|
|
The jobSetter is started by clicking on the corresponding button (1) *JobSetter*
|
|
|
|
|
|
![jobsettercall](./images/PipCon_upperpart.PNG "grid" "width:50px")
|
|
|
|
|
|
|
|
|
This will open a window
|
|
|
|
|
|
![jobsettercall](./images/jobsetter.PNG)
|
|
|
|
|
|
This wiki uses the [Markdown](http://daringfireball.net/projects/markdown/) syntax.
|
|
|
|
... | ... | |