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## [<img src="./images/up.PNG">](#back) <a name=experiment></a>Running an experiment
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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 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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> **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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The user also needs to define to which location each measurement point belongs. Two locations are pre-defined and named `nuc - nucleus` and `cyt - cytoplasm`. The locations are saved as identifier in the [xml file](#xmlfile). The locations can be different than nucleus and cytoplasm depending on the type of sample and the user can use a different name. Note that all software based on data coming from FCSrunner assumes that the locations are named `nuc` and `cyt`.
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The user also needs to define to which location each measurement point belongs. Two locations are pre-defined and named `nuc - nucleus` and `cyt - cytoplasm`. The locations are saved as identifier in the [xml file](#xmlfile). The locations can be different than nucleus and cytoplasm depending on the type of sample and the user can use a different name. Note that all software based on data coming from FCSrunner assumes that the locations are named `nuc` and `cyt`.
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... | @@ -66,7 +66,7 @@ The macro allows to acquire FCS measurements at different stage positions. For e |
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* **FCS positions**: These are the scanner positions where the FCS measurments are acquired. They are relative to the current stage position.
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* **FCS positions**: These are the scanner positions where the FCS measurments are acquired. They are relative to the current stage position.
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* **Stage positions**: The XY stage and Z-focus position.
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* **Stage positions**: The XY stage and Z-focus position.
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> Do not move the stage or focus position when placing FCS points for a cell. If you need to correct an imaging position: remove all FCS positions, change stage and focus positions and press `Update`, add the FCS positions
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FCSRunner commands | Explanations
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FCSRunner commands | Explanations
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:-----------------------------------------:|:---------
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:-----------------------------------------:|:---------
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