| ... | ... | @@ -3,8 +3,9 @@ Here we explain how to install and use Fluorescence Correlation Spectroscopy (FC |
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#### 1. [Installation](#installation)
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#### 2. [Structure of workflow](#structure-of-workflow)
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#### 3. [Prosedure](#prosedure)
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#### 3. [Prcedure](#prosedure)
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#### 4. [Interactive Visualisation of Calibration Plot](#interactive-visualisation-of-calibration-plot)
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#### 5. [Output files](#output-files)
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#### Installation
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1. Download the latest [KNIME Analytics Platform](https://www.knime.com/downloads).
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2. Install the [KNIME Python Integration](https://docs.knime.com/2018-12/python_installation_guide/index.html) to be used with KNIME Analytics Platform.
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| ... | ... | @@ -21,7 +22,7 @@ Here we explain how to install and use Fluorescence Correlation Spectroscopy (FC |
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- data processing nodes (joiner, python scripts)
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- visualisation node (Python View)
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#### Prosedure
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#### Procedure
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1. Prepare the following [structure of files](structure of files)
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2. Specify parameters in a main user input
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> You can change any parameters or leave default values. Explanation of every field can be founded in a description menu of KNIME.
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| ... | ... | @@ -37,9 +38,9 @@ Here we explain how to install and use Fluorescence Correlation Spectroscopy (FC |
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> For the execution of all nodes at one time, click on the green bottom (Execute all executable nodes) at the top of the KNIME window or just press a shortcut: Shift+F7.
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#### Interactive Visualisation of Calibration Plot
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1. Pick the point of interest in the calibration plot window to see fluctuation and correlation data from respective FCS points.
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2. Check the statistics parameters and level of bleaching at the headings of plots.
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2. The menu of the plot windows can be used to:
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1. Pick the point of interest in the calibration plot window to see fluctuation and correlation data from respective FCS points.
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2. Check the statistics parameters and level of bleaching at the headings of plots.
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2. The menu of the plot windows can be used to:
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* Save the image of the plot
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* Move and zoom a working space
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* Adjust spacing and export values from the plot
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| ... | ... | @@ -47,4 +48,23 @@ Here we explain how to install and use Fluorescence Correlation Spectroscopy (FC |
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> Sensitivity of picking event can be adjusted in the plot parameters input.
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#### Output files
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> All outputs are saved in the main directory.
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1. **info.csv**
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info.csv is generated inside the main user input. This is the main output with all final and intermediate parameters. info.csv includes:
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* the names of directories and files with fcs data
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* path to the main directory
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* calibration plot parameters and its errors
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* k - parameter that shows the intersection rate of intensity ranges of POI and FP.
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2. **calibration.csv**
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Here you can find the concentrations of POI calculated using calibration plot. Check the k-value in the info.csv after execution. k > 1 leads to less confidence in the determination of POI concentration.
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3. **calibration_plot.png**
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The image of the final calibration plot |
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