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EM Rendering - Parameters

In this section, we will cover what all of the different options in the EM renderer are, and what they do.

Base Parameters

This section covers the base parameters needed to get the Virtual Microscope to render anything.

In future sections, we will discuss optional parameters that you can use to tweak to change the final image, such as the addition of noise.

Parameter Description
PixelResolution_um X,Y size of each pixel in the final image in micrometers
ImageWidth_px X resolution of each final output image
ImageHeight_px Y resolution of each final output image
SliceThickness_um Z-height of each slice in micrometers
ScanRegionOverlap_percent Amount that each image overlaps in percentages of the image size
MicroscopeFOV_deg Currently unused, will be added in a future version
NumPixelsPerVoxel_px Allows for a sort of 'zoom', probably leave this at 1


Here is an example configuration that will render a series of 512x512 images at 10 nanometers per pixel, with a slice thickness of 20 nanometers.

EMConfig = NES.VSDA.EM.Configuration()
EMConfig.PixelResolution_um = 0.01
EMConfig.ImageWidth_px = 512
EMConfig.ImageHeight_px = 512
EMConfig.SliceThickness_um = 0.02
EMConfig.ScanRegionOverlap_percent = 0
EMConfig.MicroscopeFOV_deg = 50
EMConfig.NumPixelsPerVoxel_px = 1
VSDAEMInstance = MySim.AddVSDAEM(EMConfig)

For advanced usage and configuration of non-required parameters, please refer to other sections of this guide.

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