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### Welcome to a Wiki page of FCS pipeline! ### 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 FCS pipeline is an FCS-based calibrated image analysis software for the interactive and automated processing of FCS data.
#### 1. [Installation](#installation) #### 1. [Installation](installation)
#### 2. [Structure of workflow](#structure-of-workflow) #### 2. [Structure of workflow](#structure-of-workflow)
#### 3. [Procedure](#procedure) #### 3. [Procedure](#procedure)
#### 4. [Interactive Visualisation](#interactive-visualisation-of-calibration-plot) #### 4. [Interactive Visualisation](#interactive-visualisation-of-calibration-plot)
...@@ -47,7 +47,7 @@ CALL activate py36_knime || ECHO Activating python environment failed ...@@ -47,7 +47,7 @@ CALL activate py36_knime || ECHO Activating python environment failed
#### Procedure #### 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 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.
2. Perform FA analysis including 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** 2. Perform FA analysis including 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). 3. Prepare the following [structure of files](structure of files).
4. Specify parameters in a main user input 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. > 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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