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......@@ -6,7 +6,7 @@ Here we explain how to install and use FCS-calibrated image analysis pipeline. T
#### 3. [Procedure](#procedure)
#### 5. [Output files](#output-files)
# Structure of workflow
> Explanations of technical details of FCSpipeline you could find [here](technical details)
> Explanations of technical details of FCSpipelineEMBL_KNIME you could find [here](technical details)
**Abbreviations**:
......@@ -17,21 +17,26 @@ WT = Wild type cells containing no fluorescent protein<br>
POI = Protein of interest<br>
CPM = Counts per molecule<br>
FP = Fluorescent protein used for FCS calibration (such as monomeric GFP)
QC - Quality Check
> The main nodes users work with are typed in bold.
**Important note**: FCSpipelineEMBL_KNIME is an automated software. Only user inputs and visualization of data steps (see green frames) need the user's supervision.
![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.
#### I - WT processing block
- **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.
It calculates the background offset for the correction step in the FA. See procedure((#procedure)) below.
![12](uploads/edcfc8a40f0a1336a2158d2594da2a10/12.png)
#### II - main user input
- **plot parameters input** (calibration plot and Quality Check (QC) parameters)
This user input contains general parameters of the FCSpipelineEMBL_KNIME workflow. The explanation of every parameter can be found 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 inp.
![123](uploads/1b25493bd825b8eb77902b8217aa6add/123.png)
#### III - plot parameters input
It contains a calibration plot and QC parameters. For parameters' description go to the [input parameters](https://git.embl.de/grp-almf/FCSpipelineEMBL_KNIME/-/wikis/input-parameters) page.
#### IV - visualization block
......