Dear Dr. Yates,
Firstly, I would like to express my excitement in following your work closely. In my doctoral thesis, I conducted morphometric analyses on rats with Alzheimer's using the Quint workflow. However, due to concerns raised by my committee members regarding this workflow, I received feedback for revisions. I aligned images with an atlas template using QUICKNII and VisuAlign and performed volumetric analyses stereologically. Nonetheless, my committee members pointed out potential shrinkage or displacement during the histological preparation of samples, questioning the validity of manually fitting them to the template.

They particularly expressed concerns about errors that could arise when placing small neuroanatomical areas onto the template. They questioned how the program distinguishes local features in areas where histological boundaries are not clearly defined, even in stained sections. They inquired about the methods used in Quint workflow to validate measurement accuracy and requested information on error coefficients or standard deviations in these measurements. Furthermore, they highlighted that tissue blocks may not perfectly align with the x, y axes during sectioning by a microtome, raising questions about how axial shifts affect the placement of atlas templates and subsequent measurements.

They also asked about integrating 2D histological images into a 3D atlas and how this process ensures accuracy. Despite referencing your team’s research and providing explanations, they remained unconvinced.

Could I please ask for your assistance in addressing these concerns? Your guidance in this matter would be greatly appreciated.

Best regards,