| ... | ... | @@ -27,11 +27,11 @@ QC - Quality Check |
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The input of the individual nodes can be typed in and modified by "right click" on the node and choosing "configure". Alternatively, nodes can be opened by "double click" on the node.
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- The input of the individual nodes can be typed in and modified by "**right click**" on the node and choosing "**configure**". Alternatively, nodes can be opened by "double click" on the node.
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The source code in the individual nodes, also in the processing nodes, becomes visible by "double clicking" on the node. If needed, the scripts can be modified by the user in Python or Java.
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- The source code in the individual nodes, also in the processing nodes, becomes visible by "**double clicking**" on the node. If needed, the scripts can be modified by the user in Python or Java.
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To run a node, right click on the node and choose "execute". For the first run, we recommend the user to execute the workflow node by node, to make sure that each steps runs smoothly. Errors become visible by red light in the node and by error messages in the KNIME console.
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- To run a node, **right click **on the node and choose "**execute**". For the first run, we recommend the user to execute the workflow node by node, to make sure that each steps runs smoothly. Errors become visible by red light in the node, and /or by error messages in the KNIME console.
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#### I - WT processing block
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| ... | ... | @@ -54,7 +54,7 @@ The block provides visualization of FCSpipelineEMBL_KNIME outputs and saving of |
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**Imporatant:** FCSpipelineEMBL_KNIME deals with the outputs of Fluctuation Analyzer. 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 on the Wiki page of FCS-calibrated imaging pipeline developed by Antonio Politi.
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#### 1. Process WT FCS data with FA:
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#### 1. Process **WT** FCS data with FA:
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- Perform [import, correction, and export steps in FA](https://git.embl.de/grp-ellenberg/FCSAnalyze/-/wikis/Fa_Load_and_Correlate)
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| ... | ... | @@ -62,13 +62,13 @@ The block provides visualization of FCSpipelineEMBL_KNIME outputs and saving of |
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- Fill the WT user input and execute Python Source node. Use returned offset value (right-click -> Table) for correction steps in further FA sessions for FP and POI.
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#### 2. Perform 2 separate FA analysis sessions for FCS data on POI and FP:
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#### 2. Perform 2 separate FA analysis sessions on FCS data for **POI** and **FP**:
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- Perform [correlations calculation and correction](https://git.embl.de/grp-ellenberg/FCSAnalyze/-/wikis/Fa_Load_and_Correlate)
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- Perform [fitting of correlations with ACF](https://git.embl.de/grp-ellenberg/FCSAnalyze/-/wikis/Fa_fit_fcs)
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- Go to save, export and report step, click FA format to save corresponding res files (**mFP.res** and **POI.res**) and save (Export all traces button) fluctuation traces with ACF fitting curves for POI and FP.
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#### 3. Calculate the effective confocal volume by processing FCS data on the Dye:
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#### 3. Calculate the **effective confocal volume** by processing FCS data on the **dye**:
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- Follow the same steps described in bullet point 2 to obtain **dye.res**
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**or**
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