| ... | ... | @@ -3,12 +3,14 @@ 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. [Prosedure](#prosedure)
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#### 4. [Interactive Visualisation of Calibration Plot](interactive-visualisation-of-calibration-plot)
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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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> Take a look on [Getting Started](https://www.knime.com/knime) for a brief introduction into KNIME Analytics Platform.
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3. Save the [FCS-pipeline workflow](https://git.embl.de/halavaty/fcs-pipelines-vitali-vistunou) in knime workspace directory in your PC.
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3. Save the [FCS-pipeline workflow](https://git.embl.de/halavaty/fcs-pipelines-vitali-vistunou) in KNIME workspace directory in your PC.
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4. Install [Fluctuation Analyzer (FA) software](http://fluctuations.de/downloads.html) provided by Malte Wachsmuth.
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#### Structure of workflow
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- two user inputs:
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- main user input
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| ... | ... | @@ -20,13 +22,18 @@ Here we explain how to install and use Fluorescence Correlation Spectroscopy (FC |
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- visualisation node (Python View)
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#### Prosedure
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1. Prepare the following [structure of files](structure of files) which contains:
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* Output data from FCS experiments: .czi, .fcs, .row files produced by [ZEN software](https://www.zeiss.com/microscopy/int/products/microscope-software/zen.html)
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* Output files from [Fluctuation Analyzer (FA) software](http://fluctuations.de/downloads.html) provided by Malte Wachsmuth
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2. Fill main user input:
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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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3. Fill plot parameters input
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3. Fill a plot parameters input
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> It will implement a Quality Check by filtering the points for calibration plot according to the bounders of statistics parameters specified by user.
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4. Execute all nodes or execute different parts of pipeline sequentially
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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 |
