Question: Why did Space Ranger fail to correctly align the CytAssist image with the high resolution microscope image?
Answer: Space Ranger supports CytAssist-enabled Gene Expression analysis which uses the instrument-generated image on a CytAssist slide along with an optional high resolution microscope image of the same tissue section on a standard glass slide.
The pipeline uses an automatic image registration algorithm to align and optimize the overlay of the two image inputs. While the automatic image processing pipeline is very robust, there are cases where manual image alignment by the suer is required.
Examples of cases necessitating this include presence of shape mismatches (e.g., missing portions of the tissue section, excessive folding or tearing), or stain mismatches (e.g., excessive stain leakage, incomplete destaining, or weak re-staining) in the tissue section between the CytAssist and microscope images, manual image registration will be required.
If the tissue section is very homogenous (lacking distinct landmarks in the tissue) or the tissue is covering the fiducial markers, manual image registration may be required.
The web-summary file allows to assess the accuracy of registration using a slider to scroll/toggle between the two images.
Note: Failure of automatic image registration is not an indication of data quality or sample quality. These must be independently assessed using the appropriate QC metrics.