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...@@ -4,11 +4,13 @@ Here we explain how to install and use Fluorescence Correlation Spectroscopy (FC ...@@ -4,11 +4,13 @@ Here we explain how to install and use Fluorescence Correlation Spectroscopy (FC
#### 1. [Installation](#installation) #### 1. [Installation](#installation)
#### 2. [Structure of workflow](#structure-of-workflow) #### 2. [Structure of workflow](#structure-of-workflow)
#### 3. [Prosedure](#prosedure) #### 3. [Prosedure](#prosedure)
#### 4. [Interactive Visualisation of Calibration Plot](interactive-visualisation-of-calibration-plot)
#### Installation #### Installation
1. Download the latest [KNIME Analytics Platform](https://www.knime.com/downloads). 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. 2. Install the [KNIME Python Integration](https://docs.knime.com/2018-12/python_installation_guide/index.html) to be used with KNIME Analytics Platform.
> 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.
3. Save the [FCS-pipeline workflow](https://git.embl.de/halavaty/fcs-pipelines-vitali-vistunou) in knime workspace directory in your PC. 3. Save the [FCS-pipeline workflow](https://git.embl.de/halavaty/fcs-pipelines-vitali-vistunou) in KNIME workspace directory in your PC.
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:
- main user input - main user input
...@@ -20,13 +22,18 @@ Here we explain how to install and use Fluorescence Correlation Spectroscopy (FC ...@@ -20,13 +22,18 @@ Here we explain how to install and use Fluorescence Correlation Spectroscopy (FC
- visualisation node (Python View) - visualisation node (Python View)
![fcs_pipeline workflow](uploads/2c5fb65b19810368bcee452f8d6ea874/workflow.png) ![fcs_pipeline workflow](uploads/2c5fb65b19810368bcee452f8d6ea874/workflow.png)
#### Prosedure #### Prosedure
1. Prepare the following [structure of files](structure of files) which contains: 1. Prepare the following [structure of files](structure of files)
* Output data from FCS experiments: .czi, .fcs, .row files produced by [ZEN software](https://www.zeiss.com/microscopy/int/products/microscope-software/zen.html) 2. Specify parameters in a main user input
* Output files from [Fluctuation Analyzer (FA) software](http://fluctuations.de/downloads.html) provided by Malte Wachsmuth > You can change any parameters or leave default values. Explanation of every field can be founded in a description menu of KNIME.
2. Fill main user input:
![input1](uploads/a4c9df72fe2acfc0693cc9b274e0fba6/input1.png) ![input1](uploads/a4c9df72fe2acfc0693cc9b274e0fba6/input1.png)
3. Fill plot parameters input 3. Fill a plot parameters input
> It will implement a Quality Check by filtering the points for calibration plot according to the bounders of statistics parameters specified by user.
![input6](uploads/9722c2ef7708c222886222c7f15ad864/input6.png)
4. Execute all nodes or execute different parts of pipeline sequentially
> 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