... | ... | @@ -36,7 +36,7 @@ The compute bleach corrected correlation functions from the photon counts some p |
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<p align = 'center'> <img src="./images/rawcounts.PNG" width = "300px"> </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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For any issues please contact one of the developers in the Ellenberg group at EMBL, Heidelberg and provide the version of the software 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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... | ... | @@ -55,7 +55,7 @@ You can try this to fix |
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<a name="sectionTwo"></a>
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## [<img src="./images/up.PNG">](#back) <a name=experiment></a>Running an experiment
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Before running an experiment the user first defines imaging and FCS settings in ZEN. The macro will use these settings. When pressing one of the running options (6) the macro will acquire an image and perform the FCS measurements. In additon, an xml file is generated that contains the image coordinates.
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Before running an experiment the user first defines imaging and FCS settings in ZEN. The macro will use these settings. When pressing one of the running options the macro will acquire an image and perform the FCS measurements. In additon, an *xml* file is generated that contains the image coordinates.
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> **Imaging Settings** For FCS calibrated imaging use an uneven number of Z-slices (1, 3, 5...). This ensures that each FCS measurement corresponds to a pixel in the image.
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... | ... | @@ -70,7 +70,7 @@ The macro allows to acquire FCS measurements at different stage positions. For e |
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FCSRunner commands | Explanations
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:-----------------------------------------:|:---------
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<img src="./images/fcsRunner.PNG" width = "2000px"> | 1. Specify the number and location/type of `FCS points per object` . This information will be written in the [xml file](#xmlfile). <br/> 2. In the **FCS Positions** frame the user can `Add` FCS points to the current stage position. The other buttons will `Remove` an highlighted point or `Remove All` FCS points. In order to simplify the mapping of image and FCS position the macro forces the FCS positions to be in the center of an image pixel. <br/> 3. In the **Stage Positions** frame the user can `Add` the current stage (X,Y) and focus wheel (Z) position to the experiment. The user can `Remove` an highlighted position or `Remove All` positions. The `Update` button will update the highlighted position to the current stage (X,Y) and focus wheel (Z) position. With a double click the microscope move to the highlighted position. <br/> 4. If `One image per object` is checked then the number per FCS points at the each position does not exceed the total number of points per object. <br/> 5. Specify output directory, file format, and base file name (an optional prefix to the file name). <br/> 6. The 3 top buttons start a measurement the last stops a measurement. The difference between buttons is the order in which FCS and imaging are executed <br/> 7. Total number of FCS measurements for all positions
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<img src="./images/fcsRunner.PNG" width = "2000px"> | 1. Specify the number and location/type of `FCS points per object` . This information will be written in the [xml file](#xmlfile). <br/> 2. In the **FCS Positions** frame the user can `Add` FCS points to the current stage position. The other buttons will `Remove` an highlighted point or `Remove All` FCS points. The macro forces the FCS positions to be in the center of an image pixel. <br/> 3. In the **Stage Positions** frame the user can `Add` the current stage (X,Y) and focus wheel (Z) position to the experiment. The user can `Remove` an highlighted position or `Remove All` positions. The `Update` button will update the highlighted position to the current stage (X,Y) and focus wheel (Z) position. With a double click the microscope move to the highlighted position. <br/> 4. If `One image per object` is checked then the number per FCS points at the each position does not exceed the total number of points per object. <br/> 5. Specify output directory, file format, and base file name (an optional prefix to the file name). <br/> 6. The 3 top buttons start a measurement the last stops a measurement. The difference between buttons is the order in which FCS and imaging are executed <br/> 7. Total number of FCS measurements for all positions
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