Options

Options Tab

Figures

The Show/Save table lists all display outputs (Composite, Sticks, Histogram, Intensity):

Composite image of the variable C displays the values of C as color-coded pixels on top of the intensity image using the colors in the colormap. For a list of variables for each polarimetry method, click here
Sticks image of the variable C displays the values of C as color-coded sticks (centered around pixels) on top of the intensity image with a color given by the value of C and an orientation given by the value of ρ
Histogram displays the histograms of the selected variables C. NB: the histograms for the variables ρ (for all methods) and η (for 4POLAR 3D) are displayed as polar histograms
Intensity image displays the intensity image of the Intensity tab with the applied contrast and the selected numbered ROIs

Check the boxes in the Show column for the figure types to be displayed, and in the Save column for the figures to be saved. The format of the figures to be saved is selected using the option menu in the frame Save output.

Variables

The Variables table lists all the possible variables C. Check the boxes for the variables C to be displayed and/or saved in the analysis. See the list of variables for each polarimetry method here. The second and third columns display the minimum and maximum values of the variables used for the colorbars of histograms and composite and stick maps. These elements are editable (except for ρ) if the toggle is activated.

The colormaps for each variable are detailed here.

Preferences

The features below act interactively on displayed histograms and figures.

Checkbox Axes on figures: if ticked, the pixel numbers on the axes of each figure are displayed on the showed or saved figure images
Checkbox Colorbar on figures: if ticked, the colorbar of each composite or stick figure is displayed on the showed or saved figure images
Checkbox Colorblind-friendly: if ticked, uses colorblind-friendly colormaps on the showed or saved figure images
Spinners for the number of pixels separating sticks on stick maps: vertical = number of pixels separating sticks vertically, horizontal = number of pixels separating sticks horizontally (i.e., 1 means every pixel, 2 means every other pixel, etc...); the spinners apply directly to open stick figures
Spinner for the number of bins used in histograms (default=60, increment=5)
Button : click to open the Crop Manager

Miscellaneous tools

Button : Click this button to visualize the accuracy of the fitting per pixel. The selection of the pixel is done on the composite figure of ρ.
Button : Click this button to merge the histograms of the variables selected in the Variables table. Select the folder containing the .mat files to be concatenated.
Checkbox per ROI: if ticked, the results in histograms and in the excel files are displayed and saved separately for each ROI; otherwise, the results are displayed and saved by grouping all ROIs. It acts interactively on displayed histograms of grouped ROIs to convert them to histograms per ROI and vice versa.

Save output

The Save output table lists the saving options:

Data (.csv) for saving the values of the variables for each pixel used in the analysis as a CSV table; if the file already exists, the file is overwritten
Data (.mat) for saving the values of the variables for each pixel used in the analysis as a MATLAB .mat file
Mean values (.xlsx) for saving the mean values of the variables in a MS Excel file
Movie (.gif) for an animated gif file of the acquired stack or a region of the stack. Use the Crop Manager to define this region.

Note

The stem (i.e., filename without the extension) of the saved files is the stem of the analyzed polar stack. If the same polar stack is used for multiple analyses, the data are appended in the same MS Excel file. For a single ROI, its labels are displayed in the MS Excel file only if perROI is clicked.

Using the option menu Figures, select the format of the figures to be saved (as selected in the Figures table for the variables selected in the Variables table). Possible formats are .pdf (default), .png, .jpeg, .tif, .tif(ImageJ) (for later use in ImageJ/Fiji) and .pyfig (for later use in Open figure in PyPOLAR). The .tif(ImageJ) format saves a composite image of the intensity image and the image of the variable values per analyzed pixel. To save figures in the .tif(ImageJ) format, Save for the Composite image must be selected.

.pyfig files are PyPOLAR files storing (as a pickled file) all information on the produced figures during an analysis. This is used for minor changes in the layout of the produced figures (such as zooming, cropping, removing axes, changing colormaps, removing colorbars...) without redoing the analysis from scratch. A .pyfig file of the composite image displays the value of the selected variable (e.g., rho, psi...) per pixel in the image.

click this button to open a Jupyter notebook to visualize and personalize the appearance of colorbars used in PyPOLAR. This Jupyter notebook can be found here. For more details on this Jupyter notebook and the options to generate the colorbars, click here

reinitializes the Show/Save and Variables tables.