Step-by-Step Process of using the Aperio Scanscope to scan the pathology slides…
Recording information
1. Create a new folder under the Z drive (image_database) for the new set of slides (i.e. d00104, d00105,d00106, etc.)
2. Create a text file placed in the new folder with a description of the slides. The information usually includes the doctor that has provided some type of cells which is also indicated as well as what dye was used to stain the cells.
3. Under the Z drive (image_database), you will find a link to an excel spreedsheet named “Content.” In this spreadsheet, add the folder label you created as well as the description of what type of images will be in that folder.
Creating Labels for the Slides
4. Run ZebraDesigner 2.
5. The program will welcome you with a new label pop-up. In order to move forward, ‘Open recently used label’ should be checked and ‘C:\…\Labels\SCANNER.lbl’ chosen. Double click on the ‘C:\…\Labels\SCANNER.lbl’.
6. Left click on the barcode then right click and chose properties.
7. In the text box, change the information accordingly. (i.e. Provided by Dr. Jack Smith)
8. Close.
9. Under the barcode, left click then right click on the label, got to properties (where it says –> i.e. d00104- ???????).
10. Change the starting number if needed.
11. Change the prefix accordingly, depending on what the folder is called.
12. Under that line, left click then right click on the final line (i.e. 08/08/16 – Ki67 / H&E).
13. Update the stain under suffix.
14. Update excel spreadsheet with label number as well as patient information.
Scanning
After loading the ‘rack’ with slides, the Camera Gains should be reset. To do this, once the rack is reinserted into the scanscope, go to Tools on the upper left hand corner then Configure. Once the window is opened, go to the Motion Properties tab and click on ‘Set Line Camera Gains’. **When performing the calibration, be careful not to bump into the desk to avoid an off-focus setting!!**
Wait patiently for the Calibration to complete then close the window and continue to finish the scanning of the slides.
To Scan Indivudally
1. Click on ‘Select Rack’, right click and remove slides then rescan slides. After, right click and get snapshots.
2. Set the current slide to be scanned.
3. Under tools, configure, adjust the properties (compressiontype, compressionquality, etc) if needed (/instructed). Close.
4. Move to the Scan Area tab, adjust the parameters of the area to scan by dragging the green sides. Enclose the stained area only. Drag the blue marker to the blank area.
5. Next under Focus Points, click Autoselect and add/remove focus points to populated areas as needed.
6. Once focus points are set, click Autofocus.
7. When the scanner is through auto focus, open the Video Monitor (under view) to make fine adjustments to focus points as needed.
Check a couple of points in a couple of areas. **Remember to accept the point after viewing it.**
8. Move on to Calibrate tab, Click on ‘One Touch’.
9. The slide should be scanning, wait for it to finish.
**To scan multiple images at a time**
– Go through each image and set the desired parameters to scan within the Scan Tab, also go through the focus point process in the Focus Points tab.
– After the focus points and the parameters are set for each image then go back to the Start tab.
– In the Start tab, Select the entire rack and on the right hand bottom corner, select ‘One Touch’
– Now wait and all five slides will be scanned.
Final Image
10. After the slide is scanned, go to shortcut to images, available on the desktop. Under today’s date, you will find the image. Never click on the image while the scanner is working on it. (Check the time for the correct one to click)
11. Open the image, zoom in. Check for any bluriness.
12. Close the file. Rename it. Copy and Paste into langly.
TroubleShooting…
– if the images are appearing too light then click on the desired slide, right click to go to ‘Assign Parameter Set’ then choose ‘Gain Adjust Low’ for those images resulting in too much light (very faint, no details). For darker images, the same instructions are followed but the ‘Parameter Set’ is set to’Gain Adjust High’.