| ... | @@ -6,33 +6,6 @@ Here we explain how to install and use Fluorescence Correlation Spectroscopy (FC |
... | @@ -6,33 +6,6 @@ Here we explain how to install and use Fluorescence Correlation Spectroscopy (FC |
|
|
#### 3. [Procedure](#procedure)
|
|
#### 3. [Procedure](#procedure)
|
|
|
#### 4. [Interactive Visualisation](#interactive-visualisation-of-calibration-plot)
|
|
#### 4. [Interactive Visualisation](#interactive-visualisation-of-calibration-plot)
|
|
|
#### 5. [Output files](#output-files)
|
|
#### 5. [Output files](#output-files)
|
|
|
#### Installation
|
|
|
|
|
1. 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)
|
|
|
|
|
2. Install [Anaconda](https://www.anaconda.com/distribution/) with Python3.
|
|
|
|
|
3. 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.
|
|
|
|
|
4. Install KNIME Image Processing extension (File -> Install KNIME Extensions).
|
|
|
|
|
5. Install the KNIME Python Integration extension (File -> Install KNIME Extensions).
|
|
|
|
|
|
|
|
|
|
Follow these steps as described in [KNIME Python Integration Installation Guide](https://docs.knime.com/2018-12/python_installation_guide/index.html):
|
|
|
|
|
* Download a configuration file [fcspy.yml](https://git.embl.de/halavaty/fcs-pipelines-vitali-vistunou)
|
|
|
|
|
* Type in your terminal (for Windows use command prompt or anaconda prompt)
|
|
|
|
|
```
|
|
|
|
|
conda env create -f <PATH-TO-FOLDER-WITH-fcspy.yml>/fcspy.yml
|
|
|
|
|
```
|
|
|
|
|
* For Windows user: create py36.bat that will contain the path to your Anaconda folder (**this Anaconda folder must contain Scripts folder**):
|
|
|
|
|
```
|
|
|
|
|
@REM Adapt the folder in the PATH to your system
|
|
|
|
|
SET PATH=<PATH_TO_ANACONDA_FOLDER>\Scripts;%PATH%
|
|
|
|
|
CALL activate py36_knime || ECHO Activating python environment failed
|
|
|
|
|
@python %*
|
|
|
|
|
```
|
|
|
|
|
* For Linux users: create py36.sh with the path to your Anaconda folder (**must contain bin folder**):
|
|
|
|
|
|
|
|
|
|
6. Download [the last version of FCSpipeline](https://git.embl.de/halavaty/fcs-pipelines-vitali-vistunou) on your computer and unzip it into the knime-workspace directory where all KNIME workflows are stored.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
#### Structure of workflow
|
|
#### Structure of workflow
|
|
|
- three user inputs:
|
|
- three user inputs:
|
|
|
- main user input (general parameters)
|
|
- main user input (general parameters)
|
| ... | | ... | |
