... | ... | @@ -7,11 +7,13 @@ Here we explain how to install and use Fluorescence Correlation Spectroscopy (FC |
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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. Install [Anaconda](https://www.anaconda.com/distribution/) with Python3.
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2. Download the latest [KNIME Analytics Platform](https://www.knime.com/downloads). It is available for Windows, Linux, and Mac OS X.
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1. Install [Fluctuation Analyzer (FA) software](http://fluctuations.de/downloads.html) provided by Malte Wachsmuth.
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> In case LabVIEW error, please install [.NET Framework 3.5](https://www.microsoft.com/ru-ru/download/details.aspx?id=21)
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2. Install [Anaconda](https://www.anaconda.com/distribution/) with Python3.
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3. Download the latest [KNIME Analytics Platform](https://www.knime.com/downloads). It is available for Windows, Linux, and Mac OS X.
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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. Install KNIME Image Processing extension (File -> Install KNIME Extensions).
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4. Install the KNIME Python Integration extension (File -> Install KNIME Extensions).
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4. Install KNIME Image Processing extension (File -> Install KNIME Extensions).
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5. Install the KNIME Python Integration extension (File -> Install KNIME Extensions).
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Follow these steps as described in [KNIME Python Integration Installation Guide](https://docs.knime.com/2018-12/python_installation_guide/index.html):
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* Download a configuration file [fcspy.yml](https://git.embl.de/halavaty/fcs-pipelines-vitali-vistunou)
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... | ... | @@ -31,9 +33,9 @@ CALL activate py36_knime || ECHO Activating python environment failed |
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```
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Examples of files are [here](https://git.embl.de/halavaty/fcs-pipelines-vitali-vistunou)( (py36.bat and py35.sh)
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5. Save [fcs_pipeline.zip](https://git.embl.de/halavaty/fcs-pipelines-vitali-vistunou) on your computer and unzip it in knime-workspace directory.
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6. Download [fcs_pipeline.zip](https://git.embl.de/halavaty/fcs-pipelines-vitali-vistunou) on your computer and unzip it into knime-workspace directory.
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6. Install [Fluctuation Analyzer (FA) software](http://fluctuations.de/downloads.html) provided by Malte Wachsmuth. In case LabVIEW error, please install [.NET Framework 3.5](https://www.microsoft.com/ru-ru/download/details.aspx?id=21)
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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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... | ... | @@ -59,12 +61,11 @@ Examples of files are [here](https://git.embl.de/halavaty/fcs-pipelines-vitali-v |
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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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5. Delete point that you consider have "bad" fluctuations of fitting (list points to delete in plot parameter input.
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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 position.
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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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3. Delete point that you consider have "bad" fluctuations of fitting (list points to delete in plot parameter input.
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4. 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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