Update Home authored by Vitali Vistunou's avatar Vitali Vistunou
......@@ -21,7 +21,7 @@ Follow these steps as described in [KNIME Python Integration Installation Guide]
```
conda env create -f <PATH-TO-FOLDER-WITH-fcspy.yml>/fcspy.yml
```
* For Windows user: create py36.bat that with the path to your Anaconda folder (**must contain Scripts folder**):
* 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%
......@@ -41,8 +41,11 @@ CALL activate py36_knime || ECHO Activating python environment failed
- collecting fluctuation data (FA WT, FA FP, FA dye metanodes)
- collecting intensities (intensity data metanode)
- data processing nodes (joiner, python scripts)
- visualisation node (Python View)
![fcs_pipeline workflow](uploads/2c5fb65b19810368bcee452f8d6ea874/workflow.png)
- joiner metanode with Quality Check
- visualization node and the final table
![Untitlede](uploads/a9b4392c17927382facce75537330c6a/Untitlede.png)
#### Procedure
1. Prepare the following [structure of files](structure of files)
2. Specify parameters in a main user input
......@@ -59,9 +62,9 @@ CALL activate py36_knime || ECHO Activating python environment failed
> 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
1. Pick the point of interest in the calibration plot window to see fluctuation and correlation data from respective FCS position.
1. Pick the point of interest in the calibration plot window to see fluctuation and correlation data from the respective FCS position.
2. Check the statistics parameters and level of bleaching at the headings of plots.
3. Delete point that you consider have "bad" fluctuations of fitting (list points to delete in plot parameter input.
3. Delete points that you consider have "bad" fluctuations or quality of fitting (list points to delete in plot parameter input).
4. The menu of the plot windows can be used to:
* Save the image of the plot
* Move and zoom a working space
......@@ -82,11 +85,10 @@ info.csv includes:
* the names of directories and files with FCS data
* path to the main directory
* calibration plot parameters and its errors
* k - parameter that shows the intersection rate of intensity ranges of POI and FP
2. **calibration.csv**
Here you can find the concentrations of POI calculated using calibration plot. Check the k-value in the info.csv after execution. k > 1 leads to less confidence in the determination of POI concentration.
Here you can find the concentrations of POI calculated using calibration plot.
3. **calibration_plot.png**
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