Update Home authored by Vitali Vistunou's avatar Vitali Vistunou
......@@ -3,8 +3,9 @@ Here we explain how to install and use Fluorescence Correlation Spectroscopy (FC
#### 1. [Installation](#installation)
#### 2. [Structure of workflow](#structure-of-workflow)
#### 3. [Prosedure](#prosedure)
#### 3. [Prcedure](#prosedure)
#### 4. [Interactive Visualisation of Calibration Plot](#interactive-visualisation-of-calibration-plot)
#### 5. [Output files](#output-files)
#### Installation
1. Download the latest [KNIME Analytics Platform](https://www.knime.com/downloads).
2. Install the [KNIME Python Integration](https://docs.knime.com/2018-12/python_installation_guide/index.html) to be used with KNIME Analytics Platform.
......@@ -21,7 +22,7 @@ Here we explain how to install and use Fluorescence Correlation Spectroscopy (FC
- data processing nodes (joiner, python scripts)
- visualisation node (Python View)
![fcs_pipeline workflow](uploads/2c5fb65b19810368bcee452f8d6ea874/workflow.png)
#### Prosedure
#### Procedure
1. Prepare the following [structure of files](structure of files)
2. Specify parameters in a main user input
> You can change any parameters or leave default values. Explanation of every field can be founded in a description menu of KNIME.
......@@ -37,9 +38,9 @@ Here we explain how to install and use Fluorescence Correlation Spectroscopy (FC
> 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.
#### Interactive Visualisation of Calibration Plot
1. Pick the point of interest in the calibration plot window to see fluctuation and correlation data from respective FCS points.
2. Check the statistics parameters and level of bleaching at the headings of plots.
2. The menu of the plot windows can be used to:
1. Pick the point of interest in the calibration plot window to see fluctuation and correlation data from respective FCS points.
2. Check the statistics parameters and level of bleaching at the headings of plots.
2. The menu of the plot windows can be used to:
* Save the image of the plot
* Move and zoom a working space
* Adjust spacing and export values from the plot
......@@ -47,4 +48,23 @@ Here we explain how to install and use Fluorescence Correlation Spectroscopy (FC
> Sensitivity of picking event can be adjusted in the plot parameters input.
![calibration2](uploads/9515b50eb8729b4665a7b53b2b8852b2/calibration2.png)
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![calibration2](uploads/9515b50eb8729b4665a7b53b2b8852b2/calibration2.png)
#### Output files
> All outputs are saved in the main directory.
1. **info.csv**
info.csv is generated inside the main user input. This is the main output with all final and intermediate parameters. info.csv includes:
* the names of directories and files with fcs data
* path to the main directory
* calibration plot parameters and its errors
* k - parameter that shows the intersection rate of intensity ranges of POI and FP.
![wh](uploads/ebd9f7de8c9c6238e062c43d6d100114/wh.png)
2. **calibration.csv**
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.
3. **calibration_plot.png**
The image of the final calibration plot
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