| ... | @@ -9,18 +9,32 @@ Here we explain how to install and use Fluorescence Correlation Spectroscopy (FC |
... | @@ -9,18 +9,32 @@ Here we explain how to install and use Fluorescence Correlation Spectroscopy (FC |
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#### Installation
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#### Installation
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1. Install [Anaconda](https://www.anaconda.com/distribution/) with Python3.
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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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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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> Take a look on [Getting Started](https://www.knime.com/knime) for a brief introduction into 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. 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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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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Follow this steps:
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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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* Download a configuration file [fcspy.yml](https://git.embl.de/halavaty/fcs-pipelines-vitali-vistunou)
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* Type in your terminal (for windows command prompt or anaconda prompt)
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* Type in your terminal (for Windows use command prompt or anaconda prompt)
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```
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```
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conda env create -f <PATH-TO-FOLDER-WITH-fcspy.yml>/fcspy.yml
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conda env create -f <PATH-TO-FOLDER-WITH-fcspy.yml>/fcspy.yml
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```
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```
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conda env create -f <PATH-TO-FOLDER>/py36_knime.yml
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* For Windows user: create py36.bat that contains path to your Anaconda folder (**must contain Scripts folder**):
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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.
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```
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4. Install [Fluctuation Analyzer (FA) software](http://fluctuations.de/downloads.html) provided by Malte Wachsmuth.
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@REM Adapt the folder in the PATH to your system
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SET PATH=<PATH_TO_ANACONDA_FOLDER>\Scripts;%PATH%
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CALL activate py36_knime || ECHO Activating python environment failed
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@python %*
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```
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* For Linux users: create py36.sh that contains path to your Anaconda folder (**must contain bin folder**):
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```
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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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> fcs_pipeline directory includes all files needed for the pipeline to work.
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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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#### Structure of workflow
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- two user inputs:
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- two user inputs:
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- main user input
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- main user input
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| ... | | ... | |
