More Stitch Options

Use

To...

Rotation

Specify the rotation angle between the microscope stage coordinates and the CCD camera coordinates. Use the rotation angle to improve registration of the stitched images. You can change the default rotation with the configuration setting "STAGE_CAMERA_ROTATION_ANGLE." See softWoRx Configuration.

Pixel Size Adjustment

Set a scaling factor to improve registration of the stitched images. The default value of 1 corresponds to the standard pixel size. If the pixel size stored in the image file appears to be too small, increase the pixel size adjustment. For example, a value of 1.1 stitches the images as if the pixel size were 10% larger than indicated in the input file.

Stitch Type

Specify whether the stitching should occur along the time or Z axis. Depending upon the data collection sequence, images may either be stitched along time or Z. When possible, the stitch type is determined automatically. In some cases, you may need to specify the stitch type.

Interpolation Method

Two interpolation methods are available: Nearest Neighbor and Bilinear. Nearest Neighbor stitches images a little faster, but may lose as much as a 1/2 a pixel of image registration between adjacent panels. Although Bilinear interpolation yields more accurate spatial registration, it introduces a slight burring.

Average Overlap

Average overlapping regions among panels. Otherwise, overlapping regions contain only the last panel stitched into the corresponding region of the image.

Create Montage

Display in rows and columns a range of images acquired at different time points or Z sections. This is a good way to group multiple images into a story-board type of image when the alignment of the images is not close enough for smooth stitching.

Use

To...

Connect Panels

Smooth out discontinuities between adjacent panels. This algorithm assumes geometric alignment of the panels. If the panels you are attempting to connect are not closely aligned, you can also try adjusting the rotation or pixel size of each image to align them more closely before attempting to connect the panels.

Apply Panel Flattening

Solve the flat-field correction during the stitch process.

Background Window

Set the parameter that is related to the upper threshold of the pixel intensities that is used to calculate the panel flattening. Try increasing this value if the panel flattening fails. A background window that is too large introduces artifacts into the stitched image.

Remove Scattering Background

Subtract scattered light from each panel to minimize the intensity offset among panels. (The solution assumes that each panel has the same background, except for scattering. This option is inappropriate for images that contain a background image.)

Remove Negative Values

Set negative values to zero during the stitching process.

Make Positive

Shift the intensity of the stitched image so that all values are positive.

Fix Wrap

Fix pixel intensity wrap-around caused by a conversion from signed to unsigned integers. This is a rare condition that is not encountered during normal operation.

Remove Bright Specks

Remove bright specks from the stitched image. Adjust the Discrimination Value and the Max Width to control the size of the bright speck.

Discrimination Value

Specify the minimum intensity difference between adjacent pixels to consider as a bright speck.

Max Width

Enter the maximum allowed width (in microns) of a bright speck.

Remove Bright Pixels

Remove bight pixels from the image.

X/Y Stage Polarity

Select polarity. For DeltaVision microscopes, the polarity is
normally -/-.