Threshold
In the Threshold menu, select any number of variables for analysis with Phenoplex.
Edit Selection
To select these variables, click on Edit Selection button.
Select the variables and then click Ok.
Variables
The resulting list of variables will display the name of the variable, whether or not it is used in the phenotyping, as well as the lower threshold, and the higher threshold.
| Variable | Phenotyping | Lower Threshold | Higher Threshold |
|---|---|---|---|
| Name of the variable | Whether or not the variable is used in the phenotyping | The lower threshold for the variable | The higher threshold for the variable |
Define Cell Positivity
The Define Cell Positivity graph can be used to change the threshold of cell positivity by dragging the sliders from either left or right or by editing the values for the lower and higher threshold.
Also keep in mind that this graph is logarithmic by default, which can be changed in the lower right corner of the graph. The number of bins in the graph is 256 by default, but can be changed if needed. It is possible to zoom in on the graph by scrolling with the mouse wheel. To reset the zoom on the graph, double-click on it.
After adjusting the threshold in the graph, some of the positive cells might have turned negative. Clicking Save at the bottom of the menu saves the positivity settings to the image as the variable Threshold.
Focus View
Focus view can be used to automatically display only the channel of interest in the image. This can be done by clicking on the Focus View button.
All functionality of the Color Adjustment menu is available while in Focus View. It is possible to add additional channels to the Focus View by enabling them in the Color Adjustment menu. Any amount of channels can be enabled in the Focus View.
Changes made to channels while in Focus View will not be saved to the color channel profile.
When Focus View is complete, click on the Focus View button again to exit the Focus View. The image will return to the original saved color channel profile.
Apply saved thresholds to new images
Previously saved thresholds can be applied to new images. This can be done by loading all desired images into Phenoplex by launching Phenoplex, and then clicking the checkmark in the database for each additional image.
Ensure that the images to which thresholds are being applied have been analyzed with the same APP as the images from which the thresholds were originally saved.
A dialog box will appear indicating that the additional images are being loaded into Phenoplex. After this is done, a saved threshold can be applied to all images loaded into Phenoplex, by clicking Apply To All, which will apply the threshold of the image in question to all other images in Phenoplex.
