Scanned slide compiler

Purpose

The scanned slide compiler assembles multiple individual image-tiles acquired by slide scanning into a larger image that represents the entire area scanned.

The compiler has "batch" capabilities, meaning that if you scanned several slides and saved the output in a single folder, you can direct the scanned slide compiler to process all of the slide scans at once.

Before you start

Complete a slide scan with the option to Postpone compilation selected.

Compiling slide scans

Go to Image > Compilers and click Scanned slide.
A window titled Select the folder containing the uncompiled slide scans opens. Navigate to the folder that contains the uncompiled image tiles and click Select Folder.
Next, a window titled, Choose the folder where the images will be saved opens. Navigate to the folder in which you want to save the compiled slide scan and click Select Folder.
The Preview options window opens. Choose to run a preview of the compiled image before proceeding with the full compilation process or to skip the preview and start compiling, then click OK:
- Preview images before compiling: Check to create a preview of the compiled slide scan. If you choose this option, the compile options are not available (grayed out).
- Compile options: Available if Preview images before compiling is not selected.
  - Stitching XY: Stitching uses the image overlap to visually align individual image tiles in the X and Y orientations. It results in better image-tile alignment and cleaner compiled images—we recommend using it
  - Flatfield correction: Mitigates uneven illumination artifacts in fluorescence imaging using intelligent, image-data based correction algorithms—we recommend using it for fluorescence imaging
Depending on your choices in the previous step, you will generate either:
- a final compiled image (or images if there were multiple slide scans in the source-folder selected)
- a preview image for review—the preview image opens in the Main window along with the Slide Scan Compile with Preview dialog box.

Review the image preview and indicate how you want to proceed (click to expand):

Start Processing: Select options, then click to generate an updated preview or to compile your slide scan:
- Stitching XY: Stitching uses the image overlap to visually align individual image tiles in the X and Y orientations. It results in better image-tile alignment and cleaner compiled images—we recommend using it
- Flatfield correction: Mitigates uneven illumination artifacts in fluorescence imaging using intelligent, image-data based correction algorithms—we recommend using it for fluorescence imaging
- Compile into single image file: Check the box to compile your slide scan images into one large image.
  
  Leave the box unchecked and click Start Processing to generate an updated preview with Stitching XY and/or Flatfield correction if selected.
Postpone Compilation: Image-tile files are acquired and saved, but are not compiled into the full slide-scan image. When you're ready to compile your slide scan into a single image file, use the Scanned slide compiler (go to Image > Compilers) to compile your image.
Delete Image: Deletes the preview image.
Focus position: [displayed for 3D slide scans only] Click the buttons corresponding to different Z-positions to quickly jump to that location for review of the preview image.