The More SI Options dialog box provides the experienced DeltaVision OMX user with several parameters that may minimize image artifacts for particular data sets.
CAUTION Most SI reconstructions can be performed successfully using the settings in the main OMX SI Reconstruction dialog box. Specifying inappropriate values for these parameters may degrade the quality of the output data.
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Field |
Description |
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Skip k0 angle refinement search |
When this parameter is enabled, the reconstruction algorithm assumes the provided line-spacing and angles are correct and it does not search for a better fit. If the correct angles have been provided for all channels, enabling this setting may improve reconstruction results for low signal data. |
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Discard negative intensities |
When this parameter is enabled, all pixels with negative intensities are set to zero at the end of reconstruction. This allows the default scaling in softWoRx to be more appropriate for the data sets. |
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Shift to eliminate negative intensities |
When this parameter is enabled, at the end of reconstruction all pixel values are increased together so that the lowest intensity pixel value is equal to zero. |
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Do drift correction |
(Applies only to systems with a rotary stage.) When this parameter is enabled, prior to the start of reconstruction, the sample drift between the first and second angles and the first and third angles is calculated and corrected for. The drift values are calculated in one channel and the correction is applied to all channels. |
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Channel to use for drift correction |
Defines which channel is used to calculate the drift (1 is the first channel in the image, 2 is the second channel, etc.). The channel entered should have high signal-to-noise. If none of the channels have high signal-to-noise, the drift correction should be disabled because if the calculated drift is incorrect it will adversely affect the reconstruction. |
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Section equalization method
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Defines how varying intensities across the data are corrected for (primarily with sample bleaching). The None setting may be useful if significant camera bias drift is encountered during imaging. |
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Recalculate overlapping arrays (# of times)
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The number of times overlapping arrays are calculated. |
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Modulation amplitude factors |
First and second order modulation values. If these values are set to anything besides zero, the algorithm will not search for the modulation. Manually setting these values can be helpful when reconstructing high background data. |
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Input apodize (# of pixels, |
Defines the input apodize method. |
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Output apodize method |
Defines the output apodize method. |
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