Home.md

 ### Welcome to a Wiki page of FCS pipeline!
-Here we explain how to install and use Fluorescence Correlation Spectroscopy (FCS) pipeline. The FCS pipeline is an FCS-based calibrated image analysis software for the interactive and automated processing of FCS  data. 
+Here we explain how to install and use Fluorescence Correlation Spectroscopy (FCS) pipeline. The FCSpipeline is an FCS-based calibrated image analysis software for the interactive and automated processing of FCS  data.
 
 #### 1.  [Installation](installation)
 #### 2.  [Structure of workflow](#structure-of-workflow)
@@ -10,7 +10,7 @@ Here we explain how to install and use Fluorescence Correlation Spectroscopy (FC
 -  three user inputs:
    -  main user input (general parameters)
    -  plot parameters input (customizing your plot and setting the QC parameters)
-   -  WT user input (calculating the background offset for correction step in FA)
+   -  WT user input (calculating the background offset for correction step in Fluctuation Analyzer (FA))
 -  loading metanodes:
    -  collecting fluctuation data (FP&POI, dye metanode)
    -  loading images and coordinates (FP&POI&WT images metanode)
@@ -19,11 +19,11 @@ Here we explain how to install and use Fluorescence Correlation Spectroscopy (FC
 -  visualization nodes
 
 #### Procedure 
-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. 
+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. 
 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. 
 3.  Prepare the following [structure of files](structure of files).
-4.  Specify parameters in a main user input
-> You can change any parameters or leave default values. The explanation of every parameter can be founded in a description menu of KNIME node.
+4.  Specify parameters in the main user input
+> 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.
 
 ![input1](uploads/a4c9df72fe2acfc0693cc9b274e0fba6/input1.png)
 
@@ -58,14 +58,18 @@ info.csv is generated inside the main user input. This is the main output with a
 info.csv includes: 
 
 *  diffusion coefficient of dye and confocal volume
-*  the names of directories and files with FCS data
+*  the names of directories and files that are used in FCSpipeline
 *  path to the main directory
 *  calibration plot parameters and its errors
 
 2.  **calibration.csv**
 
-Here you can find the concentrations of POI calculated using calibration plot.  
+Here you can find the concentrations of POI calculated using calibration parameters.  
 
 3.  **calibration_plot.png**
 
 The image of the final calibration plot.
+
+4.   **calibration_plot.csv**
+
+The table with data points in calibration plot (can be used to plot the calibration plot with other software)