After image data is acquired using the DeltaVision OMX, it is reconstructed using one of two methods available in softWoRx. The primary method uses the OMX SI Reconstruction tool and is described in this topic. A second method uses the Task Builder (click the Related Topics link at the end of this procedure). Both methods can be applied to image files containing one or more sets of wavelength data.
To use the OMX SI Reconstruction tool to reconstruct SI images:
1. From the softWoRx main menu, click Process | OMX SI Reconstruction to open the OMX SI Reconstruction window.
2. Specify an input file. Choose one of the following:
Click the Input 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 Input field.
OR
Type the path and file name directly into the Input field.
NOTE The Output field will populate automatically once you specify an Input file name.
3. Choose one of the following:
Click the OMX Base OTF 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 OMX Base OTF File field.
OR
Type the path and file name directly into the OMX Base OTF File field.
The default setting for OTF file selection uses a single OTF file for processing all channels; however, you can also choose to use channel-specific OTFs:
a. Click the check box for Use Channel-Specific OTFs to enable the setting and then click Set Up OTFs to open the OMX Channel OTF Options dialog box.
b. Select the correct Image Source Drawer.
c. Click the ... button to select the OTF file to use for each channel.
d. Click OK.
4. The process for entering a background subtraction value is similar to the process used to specify an OTF. You either enter one value that will be used with all channels or one for each individual channel. Choose one of the following:
To use the default background subtraction value for all channels, leave the Background Intensity Offset field set to the default value and do not enable the Use Camera-Specific Backgrounds field.
OR
a. To specify background subtraction values for individual channels, click the check box for Use Camera-Specific Background to enable the setting and then click Set Up Background Offsets to open the OMX Camera Background Options dialog box.
NOTE Camera-specific background subtraction values override the single value entered in the Background Intensity Offset field.
b. Select the correct Image Source Drawer.
c. Enter the desired background values for each camera.
d. Click OK.
NOTE Camera-specific background subtraction values also can be specified during the acquisition process using the DeltaVision OMX software. Refer to the procedure: “To determine the acquisition parameters:” in the DeltaVision OMX User Guide.
5. Almost all images can be reconstructed using the program default settings for k0; however, in certain cases you may want to fine-tune these settings for each camera.
6. SI image reconstructions can be run immediately or added to an image processing queue. The default setting is to Run Now. If you prefer, click Run Options to display the SI Reconstruction Run Options dialog box and select a different setting. Click Close.
7. If necessary, click More Options to open the More SI Options dialog box. Set the desired fields as needed and then click Close. For most samples, these options are not needed but, in some instances, they may assist in minimizing artifacts in the images.
8. Click Do It in the main SI Reconstruction window to start the reconstruction process.