Acquire Small Animal Image
Instructions on this page are for acquiring images on a Pearl Trilogy Small Animal Imaging System using LI‑COR Acquisition Software.
Set Up page
Once you click Start, the Set Up page will open with the Detection Label dialog displayed for you to select your detection labels.
If you plan to acquire a Fast Series of image acquisitions, select only one channel. The Fast Series option works with a single channel at a time.
Detection Label Reference
| Channel | Labels | Excitation | Emission |
|---|---|---|---|
| 800 | IRDye 800CW Optical Probes (or similar) | 785 nm | 816 - 846 nm |
| 700 | IRDye 680RD Optical Probes (or similar) | 685 nm | 716 - 746 nm |
| BLI | Bioluminescence Detection | N/A | 450 - 650 nm |
| White | White Light Detection | White Light | N/A |
Acquisition Type
In the Type menu, choose from the three acquisition types available for the Pearl Imager.
Single Image
Acquire one image with any combination of channels.
Time Series
Specify how many image acquisitions that you want to acquire and how much time to wait between acquiring each image.
Fast Series
Specify the number of image acquisitions that you want to acquire, and the image acquisitions will be acquired as fast as possible.
If you have more than one channel selected when you switch to the Fast Series option, you will need to click Edit Channels and select the single channel to use for the Fast Series image acquisition.
Edit Channels
Click Edit Channels to review or change your image acquisition channel selection.
Focus Position
Select your focus position or click Determine Focus to view a series of test images (in the white light channel) at different focus positions.
Using the Determine Focus Option
If the Determine Focus button is not available, check the instrument status on the right side of the window. You may need to wait for the instrument to cool in preparation for imaging.
Click Determine Focus.
The Determine Focus Position dialog will open, and test images will be shown for you to evaluate. Test images will be shown for each of the available focus positions, so you may want to wait until a test image is visible for each focus position before choosing.
When all test images are visible, review the images. Select the focus position in the Focus Position list that corresponds to the best image and works the best for your imaging needs.
Click Set Focus Position.
Resolution
Resolution 170 µm is recommended for most scans. 85 µm and 255 µm are also available.
Default Image Information
In the Default Image Information section, add information about the images (also called metadata) that you want to be associated with all Pearl images acquired in the current imaging session. For example, if you acquire a Fast Series or Time Series of images, the default information will be associated with each image acquired in the series.
If you leave the image acquisition workflow but keep LI‑COR Acquisition open, the default information will be saved if you reconnect to the Pearl Imager. You will need to re-enter the information if you close and reopen LI‑COR Acquisition.
You can change the information for acquisitions on the Scan page and in the Image Gallery.
Instrument Setup
Options for setting up the instrument are on the right side of the LI‑COR Acquisition window. When the Pearl Imager is ready for image acquisition, the Scan button will be active and the 
icon will be shown.
For more information about setting up the Pearl and associated accessories (like the heater plate), please see the Pearl Imager Answer Portal.
Click Scan to begin acquiring images.
Scan
After clicking Scan on the Set Up page, the Scan page will open with the image acquisition process already started. When the acquisition process has completed, the Ready symbol will appear.
Viewing Image Acquisitions
Select images in the Series list to see images that are acquired.
Select Display as Acquired to automatically see the latest image as it's being acquired.
Channels of the selected acquisition are listed in the table. Select the box next to a channel to show or hide the channel.
Edit Metadata
When you acquire a series of acquisitions, the acquisitions in the series will be saved to a Collection. View Collections by opening the Image Gallery and clicking the blue dropdown arrow button to switch to the Collections view.
Click Edit Additional Information to change the default information entered on the Set Up page.
Click Edit Name to change the name of the Collection that the acquisitions will be saved to.
Repeat Acquisition Options
Click the Repeat option to acquire a new image or series with the same settings.
Click Start New to go back to the beginning of the workflow without the settings saved.
Export
In the Export To section, choose Analyze to export Zip Files that can be imported into Empiria Studio Software for analysis. Choose Publish or Present to export images in a format suitable for a journal article or slide presentation but not for analysis.
Select Include all acquisitions to export all acquisitions from a series. Without this option selected, only the acquisition that is currently selected in the Series list will be exported.
Each series is also saved as a Collection. Open the Image Gallery and switch to the Collections view to view and export Collections.