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Sample Tearing

We're able to simulate basic sample tears with the Virtual Microscope system.

Currently, we don't do anything fancy where the tears would shift over parts of the sample, it's merely an effect that's written on top of the images.

This feature has quite a few configuration options, so we will go over them here.

Parameter Description
TearingEnabled Enable or disable the generation of sample tears
TearNumPerSlice Set the baseline amount of tears per subregion slice
TearNumVariation Determine the range for sample variation, 1 would mean baseline amount ± 1
TearNumSegments Determine how many line segments each tear is made of
TearMinimumLength_um Set the minimum length for a tear, in microns
TearMaxDeltaY_um Set the maximum change in y position for this tear
TearMaxDeltaX_um Set the maximum change in x position for this tear
TearPointJitterXMax_um Maximum amount to move each segment in the x position in microns
TearPointJitterXMin_um Minimum amount to move each segment in the x position in microns
TearPointJitterYMax_um Maximum amount to move each segment in the y position in microns
TearPointJitterYMin_um Minimum amount to move each segment in the y position in microns
TearStartSize_um Set the size of the tear in microns where it starts from
TearEndSize_um Set the size of the tear in microns where it ends

Note

Due to the number of options in this feature, not all options will have an example screenshot.

Example

Enable or disable the generation of image noise.

Setting TearingEnabled to False results in the following image:

Default Render Example

EMConfig.TearingEnabled = False

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

EMConfig.TearingEnabled = True

This section covers how to set the number of tears.

The baseline number of tears, TearNumPerSlice specifies how many tears each subregion slice will have as a baseline. To vary this with randomness, use the TearNumVariation option to add randomness.

Setting TearNumPerSlice to 3 will result in the following image: Default Render Example

EMConfig.TearNumPerSlice = 180

Likewise, setting it to 1 will result in the following image: Default Render Example

EMConfig.TearNumPerSlice = 100

You can change the shape of the tears by altering the number of segments, and the jitter per segment.

More segments will allow for more complex shapes - however having too high of a jitter with many segments will cause undesirable results.

If you wish for a less linear tear shape, increasing the jitter will result in a more jagged tear.

Additionally, changing the size of the tear's width can be accomplished via the TearStartSize_um and TearEndSize_um parameters.

Setting TearNumSegments to 1 will result in the following image: Default Render Example

EMConfig.TearNumSegments = 30

Likewise, setting it to 0 will result in the following image: Default Render Example

EMConfig.TearNumSegments = 5

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Finally, if you wish to change the direction of the tear, playing with TearMaxDeltaY_um and TearMaxDeltaX_um will change the direction of travel for the tears.

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.