Here we explain how to install and use Fluorescence Correlation Spectroscopy (FCS) pipeline. The FCS pipeline is a FCS-based calibrated imaging 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)
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1. Download the latest [KNIME Analytics Platform](https://www.knime.com/downloads). It is available for Windows, Linux, and Mac OS X.
1. Download the latest [KNIME Analytics Platform](https://www.knime.com/downloads). It is available for Windows, Linux, and Mac OS X.
> Take a look on [Getting Started](https://www.knime.com/knime) for a brief introduction into KNIME Analytics Platform.
> Take a look on [Getting Started](https://www.knime.com/knime) for a brief introduction into KNIME Analytics Platform.
2. Install the [KNIME Python Integration](https://docs.knime.com/2018-12/python_installation_guide/index.html) to be used with KNIME Analytics Platform.
2. Install the [KNIME Python Integration](https://docs.knime.com/2018-12/python_installation_guide/index.html) to be used with KNIME Analytics Platform.
3. Save and unzip [fcs_pipeline.zip](https://git.embl.de/halavaty/fcs-pipelines-vitali-vistunou) in knime-workspace directory (created after KNIME installation) in your PC. fcs_pipeline directory includes all files needed for fcs pipeline to work.
3. Save and unzip [fcs_pipeline.zip](https://git.embl.de/halavaty/fcs-pipelines-vitali-vistunou) in knime-workspace directory that was created after KNIME installation. fcs_pipeline directory includes all files needed for fcs pipeline to work.
4. Install [Fluctuation Analyzer (FA) software](http://fluctuations.de/downloads.html) provided by Malte Wachsmuth.
4. Install [Fluctuation Analyzer (FA) software](http://fluctuations.de/downloads.html) provided by Malte Wachsmuth.
#### Structure of workflow
#### Structure of workflow
- two user inputs:
- two user inputs:
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@@ -57,7 +57,7 @@ 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 with FCS data
* path to the main directory
* path to the main directory
* calibration plot parameters and its errors
* calibration plot parameters and its errors
* k - parameter that shows the intersection rate of intensity ranges of POI and FP
* k - parameter that shows the intersection rate of intensity ranges of POI and FP
