... | ... | @@ -25,8 +25,6 @@ The user can specify up to 3 images that will be analysed by the plugin (Job1-3) |
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## Specify segmentation paremeters
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<div align = "center" > <img src = './images/automatedfcs2_2.png' width = "400px" > </div>
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<div align = "center" > <img src = './images/automatedfcs2_3.png' width = "400px" > </div>
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<div align = "center" > <img src = './images/automatedfcs2_4.png' width = "400px" > </div>
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1. `Main seg. Channel` Channel where to perform segmentation.
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2. `Seg. Method` Method to find threshold to separate foreground and background pixels. The name refer to the method as implemented in imageJ.
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## <a name=fcspos></a>Location of FCS measurement points
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Note that FCS measurements are only performed by MyPiC if the `Command` *setFcsPos* or *setFcsPos;focus* is specified. The points are placed so that they are as distant as possible. For example for 4 points the FCS points are located on 2 orthogonal lines.
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<div align = "center" > <img src = './images/automatedfcs2_5.png' width = "400px" > </div>
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<div align = "center" > <img src = './images/automatedfcs2_3.png' width = "400px" > </div>
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1. `FCS pts. inside obj` Number of FCS points inside object of interest. The id of these points is *nuc* for nucleus
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2. `# pixel erode` Number of erosion operations of segmented object of interest
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... | ... | @@ -54,7 +52,7 @@ Note that FCS measurements are only performed by MyPiC if the `Command` *setFcsP |
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## Test and save settings
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<div align = "center" > <img src = './images/automatedfcs2_6.png' width = "400px" > </div>
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<div align = "center" > <img src = './images/automatedfcs2_4.png' width = "400px" > </div>
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1. `Run on file` Test the analysis operations on a user defined file. The program will prompt for a file.
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2. `Load Para` Load parameter from a file named *Automated_FCS.ini*. Such a file is automatically generated when the monitoring of the directory is started.
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