| ... | @@ -84,8 +84,10 @@ The block provides visualization of FCSpipelineEMBL_KNIME outputs and saving of |
... | @@ -84,8 +84,10 @@ The block provides visualization of FCSpipelineEMBL_KNIME outputs and saving of |
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- If you calculate the effective volume with our pipeline we recommend optimizing the kappa value during the FA fitting step for dye data. For this strategy, run the fitting procedure several times with different kappa near the default meaning trying to minimize the Chi square parameter. Besides the default kappa given in the instructions of the FA fitting step, one can determine kappa experimentally.
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- If you calculate the effective volume with our pipeline we recommend optimizing the kappa value during the FA fitting step for dye data. For this strategy, run the fitting procedure several times with different kappa near the default meaning trying to minimize the Chi square parameter. Besides the default kappa given in the instructions of the FA fitting step, one can determine kappa experimentally.
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#### 4. Prepare the following [structure of files](structure of files).
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#### 4. Prepare the following [structure of files](structure of files).
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#### 5. Specify parameters in the main user input. <br>
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#### 5. Specify parameters in the main user input. <br>
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User can change the parameters or leave default ones. <br><br>
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User can change the parameters or leave default ones. <br><br>
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**Important Note:** pay attention to the **temperature** in your experiment and the **diffusion coefficient** for your dye.
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#### 6. Specify parameters in the plot parameters input.
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#### 6. Specify parameters in the plot parameters input.
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