After the OMX alignment parameters have been defined (see Defining OMX Alignment Parameters), those alignment settings are used to align the DeltaVision OMX image. The primary method used to align the image uses the softWoRx Align OMX Image tool, but the OMX Align Image task can also be added to the Task Builder. Both methods are described in this topic.
NOTE This procedure must be applied to SI, conventional, and deconvolved images, and all images with more than one channel.
Ensure that the alignment parameters have been calculated for the installed dichroic drawer, as described in Defining OMX Alignment Parameters.
To align the OMX image using the Align OMX Image tool:
1. Click Process | Align OMX Image in the softWoRx main menu to display the Align OMX Image dialog box.
2. Select an image file to align. Choose one of the following:
Click Input 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.
The dialog box reappears, this time containing the calculated alignment field data.
3. Click Image Source Drawer and, from the drop-down list, select the drawer used to acquire the image selected in Step 2.
4. Click Do It. The software will align the image using the last saved alignment parameters defined using the OMX Alignment Parameters tool.
To align the OMX image using the Task Builder:
1. From the softWoRx main menu, click Process | Task Builder to open the Processing Task Builder dialog box.
2. Select the image file(s) to align. Choose one of the following:
Click the Add Files... button and select the file(s) from the displayed list. If necessary, use the Directories and Filter fields in the Select File dialog box to navigate to the directory containing the file(s) to select.
OR
Drag-and-drop the file(s) from the Konqueror file manager into the Image Files to Process field.
3. Enable/disable the desired Processing Options.
4. Select the task, OMX Align Image, to run on the specified input file. Click Add to place the new task on the list, the minus sign to select the task, and Options to specify the parameters for that task.
Note Refer to the softWoRx Imaging Workstation User’s Manual for descriptions of the non-OMX-related tasks.
5. Click Submit to Queue. Depending on whether or not you enabled the Automatically Run the Queue option, the job will either start immediately after you click the Submit to Queue button or when you choose to run it at a later time from the softWoRx Queue Manager.