| ... | ... | @@ -10,7 +10,7 @@ Here we explain how to install and use Fluorescence Correlation Spectroscopy (FC |
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- three user inputs:
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- main user input (general parameters)
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- plot parameters input (customizing your plot and setting the QC parameters)
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- WT user input (calculating the background offset for correction step in FA)
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- WT user input (calculating the background offset for correction step in Fluctuation Analyzer (FA))
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- loading metanodes:
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- collecting fluctuation data (FP&POI, dye metanode)
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- loading images and coordinates (FP&POI&WT images metanode)
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| ... | ... | @@ -19,11 +19,11 @@ Here we explain how to install and use Fluorescence Correlation Spectroscopy (FC |
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- visualization nodes
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#### Procedure
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1. This step can be omitted. Process a WT data with Fluctuation Analyzer (FA) to obtain WT.res (only loading data and saving data steps are needed). In FCSPipeline KNIME workflow, fill a WT user input and execute Python Source node. Use returned offset value for correction steps in further FA sessions for FP and POI.
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1. This step can be omitted. Process a WT data with FA to obtain WT.res (only loading data and saving data steps are needed). In FCSPipeline KNIME workflow, fill a WT user input and execute Python Source node. Use returned offset value for correction steps in further FA sessions for FP and POI.
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2. Perform two separate sessions of FA analysis: for FP and for POI. Do all intermediate FA steps (correlations calculation, correction, fitting of correlations with ACF) to obtain mFP.res and POI.res. **Important:** do not forget to save fluctuation traces with ACF fitting curves (Export all traces button) as .cof, .itr files.
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3. Prepare the following [structure of files](structure of files).
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4. Specify parameters in a main user input
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> You can change any parameters or leave default values. The explanation of every parameter can be founded in a description menu of KNIME node.
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4. Specify parameters in the main user input
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> You can change any parameters or leave default values. The explanation of every parameter can be founded in a description menu of the KNIME node.
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| ... | ... | @@ -58,14 +58,18 @@ info.csv is generated inside the main user input. This is the main output with a |
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info.csv includes:
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* diffusion coefficient of dye and confocal volume
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* the names of directories and files with FCS data
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* the names of directories and files that are used in FCSpipeline
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* path to the main directory
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* calibration plot parameters and its errors
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2. **calibration.csv**
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Here you can find the concentrations of POI calculated using calibration plot.
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Here you can find the concentrations of POI calculated using calibration parameters.
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3. **calibration_plot.png**
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The image of the final calibration plot.
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4. **calibration_plot.csv**
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The table with data points in calibration plot (can be used to plot the calibration plot with other software) |
