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# Welcome to a Wiki page of FCSpipelineEMBL_KNIME!
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# Welcome to a Wiki page of FCSpipelineEMBL_KNIME!
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Here we explain how to install and use FCS-calibrated image analysis pipeline.
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FCSpipelineEMBL_KNIME is a software designed for automated processing: using default settings and data structure only user inputs and visualization of data steps (see green frames) need the user's supervision. In addition, the workflow allows for interactive inspection of results and offers the access and modify the source code of individual KNIME analysis nodes in Python or Java, with a flexibility to add additional processing nodes. Here we explain how to install and use FCS-calibrated image analysis pipeline.
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#### 1. [Installation](installation)
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#### 1. [Installation](installation)
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#### 2. [Structure of workflow](#structure-of-workflow)
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#### 2. [Structure of workflow](#structure-of-workflow)
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| ... | @@ -19,29 +20,8 @@ CPM = Counts per molecule<br> |
... | @@ -19,29 +20,8 @@ CPM = Counts per molecule<br> |
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FP = Fluorescent protein used for FCS calibration (such as monomeric GFP)<br>
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FP = Fluorescent protein used for FCS calibration (such as monomeric GFP)<br>
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QC - Quality Check
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QC - Quality Check
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**Important notes**:
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- FCSpipelineEMBL_KNIME is a software designed for automated processing: using default settings and data structure only user inputs and visualization of data steps (see green frames) need the user's supervision. In addition, the workflow allows for interactive inspection of results and offers the access and modify the source code of individual KNIME analysis nodes in Python or Java, with a flexibility to add additional processing nodes.
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- Before opening KNIME, we recommend to open Anaconda Navigator and check the environment by going to "environments" and choosing: py36_knime. Alternatively, one can check the environment using the Anaconda command line.
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**Open KNIME** and in the KNIME Explorer choose the FCSpipelineEMBL_KNIME worflow, which you have unzipped and placed into your local KNIME workflow directory.
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- **Comments** and detailed **information** on individual nodes with explanations on parameters and procedure are in the KNIME description panel, which appears on the right side when **clicking** on the node **once**.
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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 click** on the node. If needed, the scripts can be modified by the user in Python or Java.
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- Most of the nodes are composed of several consecutive nodes and node branches, which open up, once double clicking on the main node.
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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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#### I - WT processing block
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The WT processing block calculates the background offset for the correction step in the FA. See [the procedure](#procedure) below.
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The WT processing block calculates the background offset for the correction step in the FA. See [the procedure](#procedure) below.
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