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# Microscopy Pipeline Constructor (MyPiC)
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# Microscopy Pipeline Constructor (MyPiC)
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MyPiC is a Visual Basic for Application (VBA) macro for Zeiss confocal microscopes running with the ZEN software (version black >= ZEN2010). The macro has been developed in the group of Jan Ellenberg, EMBL, Heidelberg, and replaces the AutofocusScreenMacro.
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MyPiC is a Visual Basic for Application (VBA) macro for Zeiss confocal microscopes running with the ZEN software (version black >= ZEN2010). The macro has been developed in the group of Jan Ellenberg, EMBL, Heidelberg, and replaces the AutofocusScreenMacro.
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The macro allows
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The macro allows
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... | @@ -82,7 +82,7 @@ An example workflow using glass reflection autofocus or fluorescence based autof |
... | @@ -82,7 +82,7 @@ An example workflow using glass reflection autofocus or fluorescence based autof |
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* Glass based reflection and imaging
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* Glass based reflection and imaging
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* Fluorescence intensity center of mass based tracking
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* Fluorescence intensity center of mass based tracking
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The interaction with the adaptive feedback microscopy is exaplaied in
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The interaction with the adaptive feedback microscopy is explained in
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* [Adaptive feedback microscopy/Online image analysis](./Adaptivefeedback)
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* [Adaptive feedback microscopy/Online image analysis](./Adaptivefeedback)
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... | @@ -138,6 +138,9 @@ For each imaging and FCS [task](#task) several options can be specified. These d |
... | @@ -138,6 +138,9 @@ For each imaging and FCS [task](#task) several options can be specified. These d |
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For imaging tasks the user can specify further processing steps. For instance, the macro can compute a new XYZ position from the center of mass of the fluorescence image. The current reference position can then be updated with the computed new position (options **TrackXY** and/or **TrackZ** are on). This feature is useful to track bright objects in 3D. More complicated processing steps can be achieved when an external image analysis program is used (see also [Adaptive feedback microscopy/Online image analysis](#adaptivefeedback)).
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For imaging tasks the user can specify further processing steps. For instance, the macro can compute a new XYZ position from the center of mass of the fluorescence image. The current reference position can then be updated with the computed new position (options **TrackXY** and/or **TrackZ** are on). This feature is useful to track bright objects in 3D. More complicated processing steps can be achieved when an external image analysis program is used (see also [Adaptive feedback microscopy/Online image analysis](#adaptivefeedback)).
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> The computations `Center of mass` and `Center of mass (thr)` within MyPiC do not work with images acquired with the **Airy Detector**. To track objects using the **Airy detector** acquired images refer to the [Adaptive feedback microscopy/Online image analysis](#adaptivefeedback).
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**Task options**
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**Task options**
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<p align= center> <img src="./images/pipcon_track.PNG" width = "400px"> <p/>
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<p align= center> <img src="./images/pipcon_track.PNG" width = "400px"> <p/>
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