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Update Home authored by Vitali Vistunou's avatar Vitali Vistunou
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...@@ -32,7 +32,7 @@ Here we explain how to install and use FCS-calibrated image analysis pipeline. T ...@@ -32,7 +32,7 @@ Here we explain how to install and use FCS-calibrated image analysis pipeline. T
- Table View (concentrations of POI) - Table View (concentrations of POI)
- Two Image Viewers (loaded images with info and concentration maps) - Two Image Viewers (loaded images with info and concentration maps)
![eeffe](uploads/66713426afc1b365482a12d55d6bc87e/eeffe.png) ![wf](uploads/6b22fb7a1eddd463186cde25ee39af80/wf.png)
# Procedure # Procedure
1. Process a WT data with FA to obtain WT.res. A detailed explanation of FA analysis procedure including [correlations calculation](https://git.embl.de/grp-ellenberg/FCSAnalyze/-/wikis/Fa_Load_and_Correlate) and [fitting](https://git.embl.de/grp-ellenberg/FCSAnalyze/-/wikis/Fa_fit_fcs) can be found in git project of previous FCS-calibrated imaging pipeline developed by Antonio Politi. Only import, correction, and export steps are needed for the WT FA session. Then fill a WT user input in the KNIME workflow of FCSpipelineEMBL_KNIME and execute Python Source node. Use returned offset value for correction steps in further FA sessions for FP and POI. 1. Process a WT data with FA to obtain WT.res. A detailed explanation of FA analysis procedure including [correlations calculation](https://git.embl.de/grp-ellenberg/FCSAnalyze/-/wikis/Fa_Load_and_Correlate) and [fitting](https://git.embl.de/grp-ellenberg/FCSAnalyze/-/wikis/Fa_fit_fcs) can be found in git project of previous FCS-calibrated imaging pipeline developed by Antonio Politi. Only import, correction, and export steps are needed for the WT FA session. Then fill a WT user input in the KNIME workflow of FCSpipelineEMBL_KNIME and execute Python Source node. Use returned offset value for correction steps in further FA sessions for FP and POI.
...@@ -68,7 +68,7 @@ In Python View node of calibration plot users have an opportunity to: ...@@ -68,7 +68,7 @@ In Python View node of calibration plot users have an opportunity to:
* Reexecute the Python View node with a calibration plot * Reexecute the Python View node with a calibration plot
> Quality Check step could also help to get rid of outliers that can influence the liner parameters of the calibration line. > Quality Check step could also help to get rid of outliers that can influence the liner parameters of the calibration line.
![calibration2](uploads/9515b50eb8729b4665a7b53b2b8852b2/calibration2.png) ![vis](uploads/8db7cde8c00f138270397206e1fc0218/vis.png)
#### Hints and tips for using FCSpipelineEMBL_KNIME #### Hints and tips for using FCSpipelineEMBL_KNIME
...@@ -77,7 +77,6 @@ In Python View node of calibration plot users have an opportunity to: ...@@ -77,7 +77,6 @@ In Python View node of calibration plot users have an opportunity to:
- the execution of concentration maps metanode could take some time. If you don't need to build concentration maps, you can select all nodes except concentration maps metanode when executing pipeline. - the execution of concentration maps metanode could take some time. If you don't need to build concentration maps, you can select all nodes except concentration maps metanode when executing pipeline.
# Output files # Output files
> All outputs are saved in the main directory. > All outputs are saved in the main directory.
1. **info.csv** 1. **info.csv**
...@@ -86,6 +85,7 @@ info.csv is generated inside the main user input. This is the main output file w ...@@ -86,6 +85,7 @@ info.csv is generated inside the main user input. This is the main output file w
* the names of directories and files that are used in FCSpipeline * the names of directories and files that are used in FCSpipeline
* path to the main directory * path to the main directory
* calibration plot parameters and its errors * calibration plot parameters and its errors
* intensity baseline
2. **calibration.csv** 2. **calibration.csv**
...@@ -95,10 +95,18 @@ Here you can find the concentrations of POI in corresponding FCS positions. You ...@@ -95,10 +95,18 @@ Here you can find the concentrations of POI in corresponding FCS positions. You
The image of the final calibration plot. The image of the final calibration plot.
4. **calibration_plot.csv** ![calibration_plot](uploads/bf2c082d27346ab2be6120cdd297d08a/calibration_plot.png)
4. **cpm_distribution.png**
The image of the CPM distribution.
![cpm_distribution](uploads/32cebf67c75a3fa6efdb7ee5a467fdb6/cpm_distribution.png)
5. **calibration_plot.csv**
The table with data points in calibration plot (can be used to plot the calibration plot with other software) The table with data points in calibration plot (can be used to plot the calibration plot with other software)
5. **map folder** 6. **map folder**
The folder contains processed concentration maps in case the concentration maps metanode was used in analysis. The folder contains processed concentration maps in case the concentration maps metanode was used in analysis.