| Title | QuASI (QuPath Alignment of Serial Images) |
|---|---|
| Inputs | A set of serial or same-section whole slide images |
| Outputs | Aligned and concatenated .ome.tiffs, with optional stain deconvolution applied |
| Paper Link | N/A |
| Github Link | https://github.com/MarkZaidi/QuASI |
Description
A collection of QuPath scripts to support fully automated, whole slide image alignment, with stain separation support. Multiple same or serial-section images can be loaded into a project, including sections from different blocks, and this script will match and align the correct sections using affine-based registration techniques. The aligned image can either be previewed in the project, or written out to a .ome.tiff.
Example Images
Alignment of a Ki67 (bottom left) HDAB to a PTEN (top right) HDAB serial section. Stain deconvolution was performed along with the alignment. Aligned image shown in the top right, with deconvolved hematoxylin from PTEN (blue), DAB from PTEN (green), and DAB from Ki67 (red).
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