Scientific Volume Imaging

Background Mode is a Restoration Parameter in the Huygens Software. It establishes how the Background of an image is estimated in a deconvolution procedure.

The following choices are possible here:

• Lowest value (default): The image is searched for a 3D region with the lowest average value. The axial size of the region is around 0.3 micron; the lateral size is controlled by the radius parameter which is default set to 0.5 micron.
• In/near object: The neighborhood around the voxel with the highest value is searched for a planar region with the lowest average value.
• Widefield (WF): First the image is searched for a 3D region with the lowest values to ensure that the region with the least amount of blur contributions is found. Subsequently the background is determined by searching this region for the planar region with radius r that has the lowest value.

The size of the region where the background is looked for can be controlled by the radius parameter in the estimate background tool, but for the deconvolution commands a default value is used.

If background mode is lowest, object or wf a background value will be estimated for each channel and frame in the image. In the Batch Script, with the mode set to auto the most appropriate method for the image is selected.

The estimated values can be modified by a percentage as defined by Background Per Channel.

If the background mode is manual then the value in Background Per Channel is taken as an absolute value, and will be removed.

See BackGround.