Update Home authored by Vitali Vistunou's avatar Vitali Vistunou
...@@ -10,7 +10,7 @@ Here we explain how to install and use Fluorescence Correlation Spectroscopy (FC ...@@ -10,7 +10,7 @@ Here we explain how to install and use Fluorescence Correlation Spectroscopy (FC
- three user inputs: - three user inputs:
- main user input (general parameters) - main user input (general parameters)
- plot parameters input (customizing your plot and setting the QC 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: - loading metanodes:
- collecting fluctuation data (FP&POI, dye metanode) - collecting fluctuation data (FP&POI, dye metanode)
- loading images and coordinates (FP&POI&WT images 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 ...@@ -19,11 +19,11 @@ Here we explain how to install and use Fluorescence Correlation Spectroscopy (FC
- visualization nodes - visualization nodes
#### 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 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. 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). 3. Prepare the following [structure of files](structure of files).
4. Specify parameters in a main user input 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 KNIME node. > 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) ![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 ...@@ -58,14 +58,18 @@ info.csv is generated inside the main user input. This is the main output with a
info.csv includes: info.csv includes:
* diffusion coefficient of dye and confocal volume * 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 * path to the main directory
* calibration plot parameters and its errors * calibration plot parameters and its errors
2. **calibration.csv** 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** 3. **calibration_plot.png**
The image of the final calibration plot. 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)