# Biological Replication in MERFISH Imputation: Multiple scRNA-seq Samples onto a Single Spatial Reference **URL:** \ **Category:** General\ **Created:** [October 18, 2026, 8:02am UTC](https://community.brain-map.org/t/biological-replication-in-merfish-imputation-multiple-scrna-seq-samples-onto-a-single-spatial-reference/5113 "2026-10-18T08:02:20Z")\ **Posts on this page:** 1\ **Page:** 1
**Author:** ![Sora](https://yyz1.discourse-cdn.com/flex027/user_avatar/community.brain-map.org/sora/32/2634_2.png) [@Sora](https://community.brain-map.org/u/Sora)\ **Post date:** [October 18, 2026, 8:02am UTC](https://community.brain-map.org/t/biological-replication-in-merfish-imputation-multiple-scrna-seq-samples-onto-a-single-spatial-reference/5113/1 "2026-10-18T08:02:20Z")
Dear Allen institute team I am currently using the Zeng Aging Mouse 10Xv3 dataset, containing single-cell RNA sequencing (scRNA-seq) data from adult and aged mice. I am independently imputing data from five adult and five aged mice onto the same spatial reference, MERFISH-C57BL6J-638850, derived from a single mouse, to investigate cell-type- and region-specific transcriptional changes associated with aging. I believe this approach could provide a valuable opportunity to investigate aging-related changes across the brain within a common spatial framework. However, I recognize certain methodological limitations, particularly the use of a single mouse as the spatial reference. I would greatly appreciate your advice on what considerations, additional analyses, or validation strategies might help make this approach more scientifically robust and biologically informative. I would also be grateful if you could point me toward any previous studies employing a similar approach. Thank you very much for your time. Even brief suggestions would be greatly appreciated. Best regards, Sora Mitamura