Advanced options

Dark

The dark signal can be calculated automatically or experimentally. The default is the automatic calculation which is displayed as the Calculated dark value. The experimentally calculated dark value can be entered in the Used dark value entry box by activating the Dark toggle. For 1PF, the minimum possible value is 480.

For more details on the dark value calculation and recommendations, click here

Polarization

The value of the offset angle used in the analysis is indicated. This angle (in degrees) is measured according to the convention mentioned in the Options tab . In order to manually change this value, activate the toggle.
or : click to select the polarization direction as clockwise or counter-clockwise. The direction shown on the button is the direction chosen in the analysis.
The offset angle and the polarization direction are saved in the MS Excel file (see Save output in the Options tab).

Disk cone / Calibration data (for 1PF and 4POLAR)

For 1PF: The drop down menu lists all the disk cones included in the app. If the disk cone to be used is not in the list, select `other`and download the appropriate disk cone. The choice of disk cone also sets the value for the offset angle. Click the button to visualize the disk cone used in the `1PF` analysis. The name of the disk cone used in the analysis is displayed below the dropdown menu. The name of the disk cone is saved in the MS Excel file (see `Save output` in the Options tab).

For 4POLAR: The upper drop down menu lists all the calibration data included in the app. If the calibration data to be used is not in the list, select other and download the appropriate calibration data. The calibration data is a .txt file with a name of the type Calib*.txt containing a 4x3 matrix for 4POLAR 2D (see template) or a 4x4 matrix for 4POLAR 3D (see template). The name of the calibration data used in the analysis is displayed below the dropdown menu. Select the distribution of the polarization angles (0°, 45°, 90°, 135°) using the lower drop down menu: UL (upper left), UR (upper right), LR (lower right) and LL (lower left). The choice of distribution is saved in the MS Excel file (see Save output in the Options tab).

Binning

This option is used to improve the quality of the stack if the signal is too weak. It performs a convolution of the stack with a kernel of 1's of size Bin width x Bin height. A side effect is a blurring of the stack as displayed in the intensity images. The binning size is saved in the MS Excel file (see Save output in the Options tab).

For more information on binning, click here

Rotation

Stick (deg): (editable) value of the angle (in degrees) to arbitrarily rotate the sticks (following the convention: positive=counter-clockwise, negative=clockwise)
Figure (deg): (editable) value of the angle (in degrees) to arbitrarily rotate the entire figure (following the convention: positive=counter-clockwise, negative=clockwise)
Reference (deg): (editable) value of the angle (in degrees) with respect to which ρ is normalized; if the change of reference angle is combined with a figure rotation, the reference angle has to be determined in the rotated figure.

Intensity removal

This option is used to remove some intensity from the stack. First, define the size in pixels (`Bin width` and `Bin height`) of the bin in the part of the intensity image. Second, select a point (center of the bin of size `Bin width` x `Bin height`) in the intensity image by clicking the button . Third, choose the value `Factor` (between 0 and 1) for the fraction of the mean intensity of the bin to be removed from the stack. The mean value over the selected bin weighted by the chosen factor is removed from the entire stack. The value `Removed intensity value` which is subtracted from the stack is indicated in the lower part of the panel.