Membrane Outlines¶

Note

For this section of the guide, we will be disabling all other effects in order to clearly show each option.

Unless otherwise noted, the following configuration was used as a base for this demo:

EMConfig.GenerateImageNoise = False
EMConfig.EnableGaussianBlur = False
EMConfig.EnableInterferencePattern = False

Real Electron Microscopes create dark outlines where cell membranes are due to the staining process, the Virtual Microscope supports this as well.

Parameter	Description
`RenderBorders`	Enable or disable the rendering of cell membrane outlines
`BorderEdgeIntensity`	Intensity of the voxels at the edge of the border - lower values will darken the borders
`BorderThickness_um`	How many microns thick is the border

Example

Please note that for these examples, we use the following base configuration.

EMConfig.BorderEdgeIntensity = 75
EMConfig.BorderThickness_um = 0.06

RenderBordersBorderEdgeIntensityBorderThickness_um

Setting RenderBorders to False results in the following image:

Setting it to False will result in the following image: Default Render Example

EMConfig.RenderBorders = False

Likewise, setting it to True will result in the following image: Default Render Example

EMConfig.RenderBorders = True

Border intensity describes how light or dark to make the membrane outline - lowering this number closer to zero will make them more intense.

Setting it to 120 will result in the following image: Default Render Example

EMConfig.BorderEdgeIntensity = 120

Likewise, setting it to 20 will result in the following image: Default Render Example

EMConfig.BorderEdgeIntensity = 20

The border thickness describes how wide the membrane outline should be - higher numbers will make a larger outline. You probably don't want to make this more than 0.06um.

Setting it to 0.1um (very thick and for demonstration purposes) will result in the following image: Default Render Example

EMConfig.BorderThickness_um = 0.1

Likewise, setting it to 0.03um will result in the following image: Default Render Example

EMConfig.BorderThickness_um = 0.03

This documentation is provided by BrainGenix, a division of Carboncopies Foundation R&D. BrainGenix is a platform focused on advancing the field of whole-brain-emulation and computational neuroscience. BrainGenix is part of the CarbonCopies Foundation, a 501(c)3 non-profit organization dedicated to researching and promoting whole brain emulation. Learn more about CarbonCopies at https://carboncopies.org. For any queries or feedback regarding BrainGenix projects or documentation, please write to us at braingenix@carboncopies.org.