| ... | ... | @@ -30,7 +30,7 @@ The WT processing block calculates the background offset for the correction step |
|
|
|
|
|
|
|
#### II - main user input
|
|
|
|
|
|
|
|
The main user input contains the data input path and 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 input.
|
|
|
|
The main user input contains the 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 input.
|
|
|
|
|
|
|
|
#### III - plot parameters input
|
|
|
|
|
| ... | ... | @@ -38,7 +38,7 @@ The plot parameters input contains a calibration plot and QC parameters. For par |
|
|
|
|
|
|
|
#### IV - visualization block
|
|
|
|
|
|
|
|
The block provides visualization of FCSpipelineEMBL_KNIME outputs, inspecting the results and saving them in output folder.
|
|
|
|
The block provides visualization of FCSpipelineEMBL_KNIME outputs, inspecting the results and saving them in the output folder.
|
|
|
|
|
|
|
|
# Procedure
|
|
|
|
|
| ... | ... | @@ -50,7 +50,7 @@ The block provides visualization of FCSpipelineEMBL_KNIME outputs, inspecting th |
|
|
|
|
|
|
|
- Click FA format to save corresponding res file as **WT.res**
|
|
|
|
|
|
|
|
- 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.
|
|
|
|
- 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&POI.
|
|
|
|
|
|
|
|
#### 2. Perform 2 separate FA analysis sessions on FCS data for **POI** and **FP**:
|
|
|
|
|
| ... | ... | @@ -103,7 +103,7 @@ For the execution of all nodes at one time, press a shortcut: Shift+F7. Descript |
|
|
|
|
|
|
|
3) See the estimated concentrations of POI via FCS-calibrated imaging in the output table of **concentrations of POI** node.
|
|
|
|
|
|
|
|
4) Knime has his own Image viewer. To see raw images with concentration maps, user can right-click the Image Viewer nodes and go to View: Image Viewer. Then, double-click the image of interest.
|
|
|
|
4) Knime has his own Image viewer. To see raw images with concentration maps, users can right-click the Image Viewer nodes and go to View: Image Viewer. Then, double-click the image of interest.
|
|
|
|
|
|
|
|
|
|
|
|
|
| ... | ... | @@ -154,7 +154,7 @@ The image of the CPM distribution. |
|
|
|
|
|
|
|
5. **calibration_plot.csv**
|
|
|
|
|
|
|
|
The table with data points in calibration plot (can be used to plot the calibration plot with other software)
|
|
|
|
The table with data points in the calibration plot (can be used to plot the calibration plot with other software)
|
|
|
|
|
|
|
|
6. **map directory**
|
|
|
|
|
| ... | ... | |
