| ... | ... | @@ -21,7 +21,7 @@ Follow these steps as described in [KNIME Python Integration Installation Guide] |
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```
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conda env create -f <PATH-TO-FOLDER-WITH-fcspy.yml>/fcspy.yml
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```
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* For Windows user: create py36.bat that with the path to your Anaconda folder (**must contain Scripts folder**):
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* For Windows user: create py36.bat that will contain the path to your Anaconda folder (**this Anaconda folder must contain Scripts folder**):
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```
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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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| ... | ... | @@ -41,8 +41,11 @@ CALL activate py36_knime || ECHO Activating python environment failed |
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- collecting fluctuation data (FA WT, FA FP, FA dye metanodes)
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- collecting intensities (intensity data metanode)
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- data processing nodes (joiner, python scripts)
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- visualisation node (Python View)
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- joiner metanode with Quality Check
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- visualization node and the final table
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#### Procedure
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1. Prepare the following [structure of files](structure of files)
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2. Specify parameters in a main user input
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| ... | ... | @@ -59,9 +62,9 @@ CALL activate py36_knime || ECHO Activating python environment failed |
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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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#### 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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1. Pick the point of interest in the calibration plot window to see fluctuation and correlation data from the 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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3. Delete point that you consider have "bad" fluctuations of fitting (list points to delete in plot parameter input.
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3. Delete points that you consider have "bad" fluctuations or quality 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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| ... | ... | @@ -82,12 +85,11 @@ info.csv includes: |
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* the names of directories and files with FCS data
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* path to the main directory
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* calibration plot parameters and its errors
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* k - parameter that shows the intersection rate of intensity ranges of POI and FP
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2. **calibration.csv**
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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.
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Here you can find the concentrations of POI calculated using calibration plot.
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3. **calibration_plot.png**
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The image of the final calibration plot. |
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\ No newline at end of file |
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The image of the final calibration plot. |
