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6. Decon Settings

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Matthew Mueller edited this page May 30, 2024 · 13 revisions

1. Decon Settings Tab

Decon Settings

  1. Checking the Decon Only box will let you access this tab from the Next/Previous buttons
  2. RL Method will let you choose the method for decon. OMW is recommended and can use GPU acceleration if a GPU is available. Original will use original Matlab Richardson Lucy. Simplified will use a faster version of Richardson Lucy that has GPU acceleration if a GPU is available.
    1. Wiener Aplha, OTF Cumulative Threshold, Hann Win Bounds, and Manual Skewed Selection are only available when using the OMW Decon Method
  3. Wiener Aplha is the Wiener Alpha value for the OMW method
  4. OTF Cumulative Threshold is the threshold value for the OTF segmentation (0-1)
  5. Hann Win Bounds is the lower and upper bound for the anodization (0 is the center and 1 is the edge)
  6. Manual Skewed Selection allows you to define whether you are doing the deconvolution in the skewed space (If this value is not set then it will try to automatically determine whether it is in the skewed space or not)
  7. The PSF Full Paths button will open up a window where full paths to the PSF files can be selected
    1. A PSF Path should be the full path to a single tiff file
    2. PSF Paths will line up with their associated channel.
  8. Set PSF Step Size (dz for PSF) as needed
  9. Generate PSF will attempt to generate a new PSF based on the provided PSF when checked
  10. Decon Iterations will let you set the max number of Decon Iterations when using the stop criteria (Default) or the exact number of iterations to be performed when using Fixed Iter (See Decon Advanced Settings)
  11. Set Background Intensity as needed
  12. GPU Job will try to use a GPU if available when checked

2. Decon Advanced Settings

Decon Advanced Settings

  1. Debug Mode will produce decon results every Save Step iterations (I.E. if Save Step is 5 then every 5 iterations)
    1. Debug Mode is not available when using the Original method
  2. Large Method means the large scale processing method will be used
  3. Edge Erosion is the number of voxels from the edge to exclude. This is for removing edge artifacts. Checking Erode By FTP as true will use the first time point and the first channel to remove the edge artifacts.
  4. Decon Rotate will rotate decon results within the deconvolution steps
  5. Damper Factor is the factor to reduce the signal amplification from the deconvolution
  6. Decon Offset is the offset applied after deconvolution (I.E. to make the background not zero)
  7. Scale Factor is the factor to amplify or reduce the signal after deconvolution
  8. Decon Mask Files are the MIP masks that allow empty regions to be skipped
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