Hello, I am working with a scRNAseq dataset of the hypothalamus, which I annotated with MapMyCells. Based on this, when I subcluster the tanycytes population I get one subcluster with all cells being part of the 1173_tanycyte annotation, while the other subcluster being made by 1174_tanycytes.
When I go and look for these annotations in the ABC spatial map, I can see that those correspond anatomically to the alpha and beta subpopulations of tanycytes in a very precise manner as it can be seen in the links at the end of the post. Now after this great result being facilitated by the atlas, I would like to include it in the paper resulting from this research and I would like to know which is the correct way to use these resources in our publications.
Thanks for your help!
@Pablo_ValderramaC
That is very exciting! We’re so glad that MapMyCells helped you in your research.
For the moment*, the correct way to cite MapMyCells is to use the RRID citation (it’s like a DOI for software). See this page, specifically I think you would include something like MapMyCells (RRID:SCR_024672) in your bibliography.
It would probably also be appropriate to cite Yao et al. 2023, since the algorithm was originally developed for that paper.
*There is a plan in the works to write a MapMyCells-dedicated paper. I do not know if it will be out soon enough to accommodate your timeline. I’ll post again here when it is out, just in case.
Also, there is an RRID for citing ABC Atlas (which it sounds like you used to find the spatial correspondence to your cell types)
Allen Brain Cell Atlas (RRID:SCR_024440) Allen Brain Cell Atlas - brain-map.org
Full RRID page here
Hello Daniel,
Thanks for the information! I was also wondering if there is a way to use like the images coming from the ABC Atlas in our paper as a support for the annotation of my subclusters? There is a colleague in the lab that went to a workshop of the Allen Institute in Seattle and they encouraged doing it, but we don’t know if there is a correct way that you recommend or support for doing it, apart from citing the tool and paper.
There is a button that allows you to download your current view as a PNG (see this post).
Does that get you what you need?