This topic describes how to open a scanned bead data file and save it as an OTF file that can be used for image reconstruction.
For information discussing how to create and scan a bead slide, refer to the DeltaVision OMX User Guide.
Scanned bead data file
To create an OTF file:
1. Click Process | Make OMX OTF in the softWoRx main menu. This will open the OMX Create OTF dialog box.
2. Specify an input PSF file. Choose one of the following:
Click the PSF File button and select a file from the displayed list. If necessary, use the Directory field and/or navigation icons in the Select File dialog box to navigate to the directory containing the desired file.
OR
Drag-and-drop a file from the Konqueror file manager into the PSF File field.
OR
Type the path and file name directly into the PSF File field.
NOTE The OTF File field populates automatically once you specify the PSF File name.
3. If you did not specify a bias/background value when you acquired the bead data file, specify an appropriate value in the Background to subtract field.
4. Ensure that the Enable Leave KZ capability checkbox is disabled (empty).
5. Ensure that the Do bead compensation calculation checkbox is enabled (checked) and that the Bead diameter field displays the correct value.
NOTE Only very rarely will you need to modify the default values for the Line spacing and k0 angles fields.
6. Ensure that the Show OTF image when finished checkbox is enabled.
7. Click Do It. The software will create an initial OTF image file and, when processing is complete, display that file in an image window for viewing.
8. Scale the OTF image shown in the image window for viewing. Typical values for the Display Min/Max/Exp field are “00 10 3”.
9. View the OTF Orders created (Z=1, Z=2, Z=3). These images will help you determine the Leave KZ (cleaning) values.
View OTF Orders
10. Return to the OMX Create OTF dialog box and enable (check) the Enable Leave KZ capability checkbox, as shown in the following figure.
Leave KZ Fields
11. Determine the three Leave KZ values by calculating the number of pixels along the edges of the feathers, as described in the following steps. Then, enter these values into the corresponding Leave KZ fields in the OMX Create OTF dialog box shown in the previous figure.
a. Determine the value for Leave KZ field a by counting the number of pixels from the left-bottom corner of the feather image to the left-bottom edge of the feather in the “2nd section, 1st order” image. Enter the value into Field a.
b. Determine the value for Leave KZ field b by counting the number of pixels from the left-bottom corner of the feather image to the right edge of the feather, also in the “2nd section, 1st order” image. Enter the value into Field b.
Define Fields a and b Using 2nd Section, 1st Order
c. Determine the value for Leave KZ field c by counting the number of pixels from the right-bottom corner of the feather image to the edge of the brightest portion of the feather tip, in the “3rd section, 2nd order” image. Usually, this value will be two to three pixels. Enter the value into Field c.
Define Field c Using 3rd Section, 2nd Order
12. In the OMX Create OTF dialog box, click Do It to recreate the OTF with the Leave KZ values you just entered.
13. When the new OTF opens in the image window, check to make sure too much cleaning did not occur. The brightest portion of the feather tips should still be intact, as shown in the following figure.
Cleaned OTF Orders
14. Use the newly generated OTF to reconstruct an image.