When a matrix is active, you can use the Palette button and the Missing Value Color button to customize color of the matrix window.
Origin provides multiple build-in graph types for presenting NetCDF data. They are all available from the Plot menu
Recommended Tutorials for Further Graph Customization
You can use the Climate template to plot the NetCDF data.
Select Plot: Template Library to open the dialog. Select Climate template and click Plot button.
Origin supports creating contour plots in spherical surface projections. Please refer to the tutorial below for detailed steps
After creating an image or contour graph, you can click the Graph Browser button. The Browser Graph has a panel on the left-side of the window that is used to select the plots from the NetCDF matrix stack.