... | ... | @@ -198,13 +198,13 @@ where |
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Each well is saved in a separate directory
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``` DE_WXXXX_PYYYY```
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``` DE_WXXXX_PYYYY ```
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If number of subpositions is > 1 then there is a subdirectory per subposition
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```
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```
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DE_WXXXX
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DE_WXXXX_PYYYY
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DE_WXXXX_PYYYY
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```
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## [<img src="./images/up.PNG">](#back) <a name=startstop></a> Start and stop acquisition, save and load settings
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... | ... | @@ -255,7 +255,7 @@ Contains the commands for the microscope |
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`setRoi` | Read ROIs and update ROIs for subsequent task(s) in pipeline
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<a name="codeoia"></a>
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####Key **CodeOia**
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#### Key **CodeOia**
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Contains commands for the image analysis program.
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Value | Meaning
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... | ... | @@ -264,7 +264,7 @@ Contains commands for the image analysis program. |
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`newImage` | A new image with path filePath needs to be analysed
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<a name="filepath"></a>
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####Key **filePath**
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#### Key **filePath**
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Contains full path of image that needs to be analysed
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Value | Meaning
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... | ... | @@ -274,7 +274,7 @@ Contains full path of image that needs to be analysed |
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<a name="xyz"></a>
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####Keys **XYZ**
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#### Keys **XYZ**
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Specifies stage positions. Coordinates with respect to upper left corner of the image (in pixels) and first slice (0,0,0). Several points are separated by `;`
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Value | Meaning
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... | ... | @@ -283,7 +283,7 @@ Specifies stage positions. Coordinates with respect to upper left corner of the |
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`Y1;Y2;Y3;...` | Y positions with respect to upper corner in pixels
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`Z1;Z2;Z3;...` | Z positions with respect to bottom slice in pixels. If this key is left empty current focus position is used.
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####Keys **fcsX**, **fcsY**, **fcsZ**
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#### Keys **fcsX**, **fcsY**, **fcsZ**
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Specifies FCS scanner positions. Coordinates with respect to upper left corner of the image (in pixels) and first slice (0,0,0). Several points are separated by `;`
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... | ... | @@ -296,7 +296,7 @@ Specifies FCS scanner positions. Coordinates with respect to upper left corner o |
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<a name="rois"></a>
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####Keys **roiAim**, **roiType**, **roiX**, **roiY**
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#### Keys **roiAim**, **roiType**, **roiX**, **roiY**
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A ROI is defined by 4 different keys.
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Value | Meaning
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... | ... | |