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Update Home authored by Vitali Vistunou's avatar Vitali Vistunou
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......@@ -19,6 +19,12 @@ CPM = Counts per molecule<br>
FP = Fluorescent protein used for FCS calibration (such as monomeric GFP)
> The main nodes users work with are typed in bold.
![wf3](uploads/3e13219973e4aabd25390e25c2c0e788/wf3.png)
**Important note**: FCSpipelineEMBL_KNIME is an automated software. Only user input and visualization of data steps (see green frames) need the user's supervision.
- **main user input** (general parameters). The explanation of every parameter can be founded on the [input parameters](https://git.embl.de/grp-almf/FCSpipelineEMBL_KNIME/-/wikis/input-parameters) page or in a KMIME description menu of the main user input.
![12](uploads/edcfc8a40f0a1336a2158d2594da2a10/12.png)
......@@ -27,25 +33,7 @@ FP = Fluorescent protein used for FCS calibration (such as monomeric GFP)
![123](uploads/1b25493bd825b8eb77902b8217aa6add/123.png)
- WT user input (for calculating the background offset for the correction step in the Fluctuation Analyzer (FA))
- Loading the data:
- FP&POI, dye metanodes (collecting fluctuation data)
- FP&POI&WT images metanode (loading images and coordinates)
- Data processing + Quality Check:
- Python Script (2=>1) (calculating confocal volume and concentrations)
- intensity calculation metanode (extracting intensities in ROI-s, background subtraction)
- joiner metanode with Quality Check (data collection for calibration plot + Quality Check)
> It will implement a Quality Check by filtering the points for calibration plot according to the bounders of statistics parameters specified by the user in plot parameters input.
- concentration map metanode (building concentration maps from row images using calibration parameters)
- Visualization of data
- Python Source (POI&FP CPM distribution)
- **Python View** (calibration plot appears when you execute this node)
- Table View (concentrations of POI)
- Two Image Viewers (loaded images with info and concentration maps)
**Important note**: FCSpipelineEMBL_KNIME is an automated software. Only user input and visualization of data steps need the user's supervision.
![wf](uploads/6b22fb7a1eddd463186cde25ee39af80/wf.png)
# 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) you can find on git page of FCS-calibrated imaging pipeline developed by Antonio Politi. Perform import, correction, and export steps in FA. 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.
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