8. Acquire alignment images

1. Path: Select a folder to store these high-power images. These are the reference images you will compare to lookup images to decide whether to count the object or not.
2. File Base Name: Used while naming the images that are saved.
3. Format: Select an image type.
4. Click the Gather Reference Images button: High-power images (for which the image size was set at step 4) are acquired from the reference section at systematic random locations.
5. Once all images have been acquired:
   • The message "Images Successfully Acquired" appears below the Gather Reference Images button.
   • The reference image is displayed with the contour.

Focus at Each Site:

Allows you to adjust the Z-plane for each high-power reference image acquired. Select None or Pausing for Manual Focus.

Store Acquired Images:

• Path: Select a folder to store these high-power images. These are the reference images you will compare to lookup images to decide whether to count the object or not.
• File Base Name: Used while naming the images that are saved.
• Format: Select an image type.

Multichannel Acquire:

If you're acquiring multiple fluorescent channel images for each site, check Multichannel Acquire.

You may need a time delay while the stage settles down after a move.

Acquire Images:

1. When ready to acquire the images, click Gather Reference Images. The stage drives to each site and prompts you to focus on the section (unless you selected None from Focus at Each Site).
2. Click OK.
3. Repeat until all sites have been visited and reference images acquired.