# Using ABC atlas for publications **URL:** \ **Category:** Allen Brain Cell (ABC) Atlas\ **Created:** [July 15, 2025, 5:48pm UTC](https://community.brain-map.org/t/using-abc-atlas-for-publications/4530 "2025-07-15T17:48:14Z")\ **Posts on this page:** 5\ **Page:** 1
**Author:** ![Pablo\_ValderramaC](https://avatars.discourse-cdn.com/v4/letter/p/9f8e36/32.png) [@Pablo\_ValderramaC](https://community.brain-map.org/u/Pablo_ValderramaC)\ **Post date:** [July 15, 2025, 5:48pm UTC](https://community.brain-map.org/t/using-abc-atlas-for-publications/4530/1 "2025-07-15T17:48:14Z")
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! > **[Brain Knowledge Platform](https://knowledge.brain-map.org/abcatlas#AQEBSzlKTjIzUDI0S1FDR0s5VTc1QQACSFNZWlBaVzE2NjlVODIxQldZUAADBAFGUzAwRFhWMFQ5UjFYOUZKNFFFAAIAAAFRWTVTOEtNTzVITEpVRjBQMDBLAAIAAAExNUJLNDdEQ0lPRjFTTExVVzlQAAIBMTE3MyBUYW55Y3l0ZSBOTl8yAAABQ0JHQzBVMzBWVjlKUFI2MFRKVQACAAAEAQACggSIToPW7qADgcQ6SoDIhIcEMk5RVElFN1RBTVA4UFFBSE80UAAFga%2BmSoHprA6BoIFHgJLV6AYABwAABQAGAQECRlMwMERYVjBUOVIxWDlGSjRRRQADfgAAAAQAAAhWRk9GWVBGUUdSS1VEUVVaM0ZGAAlMVkRCSkFXOEJJNVlTUzFRVUJHAAoACwFUTE9LV0NMOTVSVTAzRDlQRVRHAAI3M0dWVERYREVHRTI3TTJYSk1UAAMBBAEAAiMwMDAwMDAAA8gBAAUBAQIjMDAwMDAwAAPIAQAAAAIBAA%3D%3D%E2%80%8B)** > **[Brain Knowledge Platform](https://knowledge.brain-map.org/abcatlas#AQEBSzlKTjIzUDI0S1FDR0s5VTc1QQACSFNZWlBaVzE2NjlVODIxQldZUAADBAFGUzAwRFhWMFQ5UjFYOUZKNFFFAAIAAAFRWTVTOEtNTzVITEpVRjBQMDBLAAIAAAExNUJLNDdEQ0lPRjFTTExVVzlQAAIBMTE3NCBUYW55Y3l0ZSBOTl8zAAABQ0JHQzBVMzBWVjlKUFI2MFRKVQACAAAEAQACggSIToPW7qADgcI6SoDIhIcEMk5RVElFN1RBTVA4UFFBSE80UAAFga%2BmSoHprA6BoIFHgJLV6AYABwAABQAGAQECRlMwMERYVjBUOVIxWDlGSjRRRQADfgAAAAQAAAhWRk9GWVBGUUdSS1VEUVVaM0ZGAAlMVkRCSkFXOEJJNVlTUzFRVUJHAAoACwFUTE9LV0NMOTVSVTAzRDlQRVRHAAI3M0dWVERYREVHRTI3TTJYSk1UAAMBBAEAAiMwMDAwMDAAA8gBAAUBAQIjMDAwMDAwAAPIAQAAAAIBAA%3D%3D%E2%80%8B)** ---
**Author:** ![danielsf](https://yyz1.discourse-cdn.com/flex027/user_avatar/community.brain-map.org/danielsf/32/209_2.png) [@danielsf](https://community.brain-map.org/u/danielsf)\ **Post date:** [July 15, 2025, 7:42pm UTC](https://community.brain-map.org/t/using-abc-atlas-for-publications/4530/2 "2025-07-15T19:42:54Z")
@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,](https://rrid.site/data/record/nlx_144509-1/SCR_024672/resolver?q=MapMyCells&l=MapMyCells&i=rrid:scr_024672) 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,](https://www.nature.com/articles/s41586-023-06812-z) 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. ---
**Author:** ![danielsf](https://yyz1.discourse-cdn.com/flex027/user_avatar/community.brain-map.org/danielsf/32/209_2.png) [@danielsf](https://community.brain-map.org/u/danielsf)\ **Post date:** [July 15, 2025, 8:06pm UTC](https://community.brain-map.org/t/using-abc-atlas-for-publications/4530/3 "2025-07-15T20:06:30Z")
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](https://portal.brain-map.org/atlases-and-data/bkp/abc-atlas) [Full RRID page here](https://rrid.site/data/record/nlx_144509-1/SCR_024440/resolver?q=ABC%2520Atlas&l=ABC%2520Atlas&i=rrid:scr_024440) ---
**Author:** ![Pablo\_ValderramaC](https://avatars.discourse-cdn.com/v4/letter/p/9f8e36/32.png) [@Pablo\_ValderramaC](https://community.brain-map.org/u/Pablo_ValderramaC)\ **Post date:** [July 16, 2025, 7:26pm UTC](https://community.brain-map.org/t/using-abc-atlas-for-publications/4530/4 "2025-07-16T19:26:48Z")
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. ---
**Author:** ![danielsf](https://yyz1.discourse-cdn.com/flex027/user_avatar/community.brain-map.org/danielsf/32/209_2.png) [@danielsf](https://community.brain-map.org/u/danielsf)\ **Post date:** [July 16, 2025, 8:33pm UTC](https://community.brain-map.org/t/using-abc-atlas-for-publications/4530/5 "2025-07-16T20:33:10Z")
There is a button that allows you to download your current view as a PNG (see [this post](https://community.brain-map.org/t/abc-atlas-user-guide/3179#p-5675-download-image-15)). Does that get you what you need?