Staff Profiles

Song-Lin Ding, M.D.

Principal Scientist

Song-Lin Ding joined the Allen Institute in 2010 as a chief neuroanatomist to create reference atlases for the developing and adult human brains. He also generates brain ontology and defines laser microdissection sampling areas for human and macaque brain structures in various stages of development. Ding has over 23 years of experience in neuroanatomy. Prior to joining the Allen Institute, Ding served as a research scientist at the University of Iowa and a Research Assistant Professor at the University of Rochester. In both places, he focused on anatomical organization of adult human and macaque brains. At the University of Iowa he also helped characterize a mouse model for Batten Disease. Prior to this work, Ding was an Associate Professor at the Institute of Neuroscience, Guangzhou Medical College, China where he investigated the development of human visual and hippocampal cortices. His research interests mainly cover connectional, chemical, developmental and comparative aspects of the visual and limbic systems. His postdoctoral work at the Center for Neuroscience at the University of Tennessee, Memphis focused on the development and chemical natures of the corpus callosum connections in the rat and cat visual cortex. Ding received a M.D. from Hunan Medical University in China. He is also a Guest Professor at the Institute of Neuroscience, Guangzhou Medical College, China.


Research Interests

Research Interests Understanding detailed brain organization – including its cell types, chemical/molecular nature, connections and parcellations – is an essential step to revealing the mechanisms underlying different brain functions and related diseases. As a neuroanatomist, I am interested in generating anatomical and molecular atlases for the developing and adult human and macaque brains. We use these atlases to guide our large-scale laser microdissection efforts at the Allen Institute. To create precise and detailed human brain reference atlases I use a combination of cellular and molecular markers in multiple cell types to identify the chemical characterization, molecular signature, and unique developmental changes of each target brain structure. So far we have created the first version of digital reference atlases for one adult and two prenatal human brains. Our ongoing effort is to generate reference atlases with more detailed parcellation of the entire human brain by adding fine cortical and subcortical subdivisions. Anatomical and molecular atlases of developing macaque brains provide exemplary models where there is very limited availability of human brains in various stages of development. To collect large-scale microarray data on macaque brain development we are now trying to define all layers of the visual, somatosensory and anterior cingulate cortices as well as subdivisions of the hippocampal formation, amygdala and basal ganglia at six stages of prenatal development. This dataset, together with the microarray data from prenatal human brains, will significantly fuel our understanding of human brain development and related disease. One of my future goals is to explore comparative neuroanatomy of human, monkey and rodent brains with emphasis on the visual and limbic structures. I aim to compare cell types and their molecular characterization, wiring circuits and developmental changes in different species in order to gain information on similarities and differences among these species. In addition, searching for mouse cortical homologues of human and macaque brains using molecular and connectional neuroanatomy would greatly facilitate the interactive use of the huge datasets created at the Allen Institute for mouse, macaque and human brains.


  • Neuroanatomy
  • Brain development
  • Atlasing
  • Neurodegenerative disease

Research Programs

  • Cell types
  • Atlasing

Selected Publications View Publications

Distinct Transcriptomic Cell Types and Neural Circuits of the Subiculum and Prosubiculum along the Dorsal-Ventral Axis

Cell Reports
May 19, 2020

Ding SL, Yao Z, Hirokawa KE, Nguyen TN, Graybuck LT, Fong O, Bohn P, Ngo K, Smith KA, Koch C, Phillips JW, Lein ES, Harris JA, Tasic B, Zeng H

The Allen Mouse Brain Common Coordinate Framework: A 3D Reference Atlas

May 14, 2020

Wang Q, Ding SL, Li Y, Royall J, Feng D, Lesnar P, Graddis N, Naeemi M, Facer B, Ho A, Dolbeare T, Blanchard B, Dee N, Wakeman W, Hirokawa KE, Szafer A, Sunkin SM, Oh SW, Bernard A, Phillips JW, Hawrylycz M, Koch C, Zeng H, Harris JA, Ng L

Afferent Projections to Area Prostriata of the Mouse

Frontiers in Neuroanatomy
November 27, 2020

Hu JM, Chen CH, Chen SQ, Ding SL.

Homotopic Commissural Projections of Area Prostriata in Rat and Mouse: Comparison With Presubiculum and Parasubiculum

Frontiers in Neural Circuits
November 13, 2020

Chen CH, Hu JM, Chen SQ, Liu SM, Ding SL.

Conserved cell types with divergent features in human versus mouse cortex

August 21, 2019

Hodge RD, Bakken TE, Miller JA, Smith KA, Barkan ER, Graybuck LT, Close JL, Long B, Johansen N, Penn O, Yao Z, Eggermont J, Höllt T, Levi BP, Shehata SI, Aevermann B, Beller A, Bertagnolli D, Brouner K, Casper T, Cobbs C, Dalley R, Dee N, Ding SL, Ellenbogen RG, Fong O, Garren E, Goldy J, Gwinn RP, Hirschstein D, Keene CD, Keshk M, Ko AL, Lathia K, Mahfouz A, Maltzer Z, McGraw M, Nguyen TN, Nyhus J, Ojemann JG, Oldre A, Parry S, Reynolds S, Rimorin C, Shapovalova NV, Somasundaram S, Szafer A, Thomsen ER, Tieu M, Quon G, Scheuermann RH, Yuste R, Sunkin SM, Lelieveldt B, Feng D, Ng L, Bernard A, Hawrylycz M, Phillips JW, Tasic B, Zeng H, Jones AR, Koch C, Lein ES

Localization of area prostriata and its connections with primary visual cortex in rodent

Journal of Comparative Neurology
August 19, 2019

Lu W, Chen S, Chen X, Hu J, Xuan A, Ding SL

Progress update from the hippocampal subfields group

Alzheimers & Dementia
June 13, 2019

Olsen RK, Carr VA, Daugherty AM, La Joie R, Amaral RSC, Amunts K, Augustinack JC, Bakker A, Bender AR, Berron D, Boccardi M, Bocchetta M, Burggren AC, Chakravarty MM8, Chételat G, de Flores R, DeKraker J, Ding SL, Geerlings MI, Huang Y, Insausti R, Johnson EG, Kanel P, Kedo O, Kennedy KM, Keresztes A, Lee JK, Lindenberger U, Mueller SG, Mulligan EM, Ofen N, Palombo DJ, Pasquini L, Pluta J, Raz N, Rodrigue KM, Schlichting ML, Lee Shing Y, Stark CEL, Steve TA, Suthana NA, Wang L, Werkle-Bergner M, Yushkevich PA, Yu Q, Wisse LEM

Automated segmentation of medial temporal lobe subregions on in vivo T1-weighted MRI in early stages of Alzheimer's disease

Human Brain Mapping
April 29, 2019

Xie L, Wisse LEM, Pluta J, de Flores R, Piskin V, Manjón JV, Wang H, Das SR, Ding SL, Wolk DA, Yushkevich PA

Characterization of hippocampal subfields using ex vivo MRI and histology data: Lessons for in vivo segmentation

November 1, 2019

de Flores R, Berron D, Ding SL, Ittyerah R, Pluta JB, Xie L, Adler DH, Robinson JL, Schuck T, Trojanowski JQ, Grossman M, Liu W, Pickup S, Das SR, Wolk DA, Yushkevich PA, Wisse LEM

Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type

Nature Neuroscience
August 27, 2018

Boldog E, Bakken TE, Hodge RD, Novotny M, Aevermann BD, Baka J, Bordé S, Jennie L. Close, Diez-Fuertes F, Ding SL, Faragó N, Kocsis AK, Kovács B, Maltzer Z, McCorrison JM, Miller JA, Molnár G, Oláh G, Ozsvár A, Rózsa M, Shehata SI, Smith KA, Sunkin SM, Tran DN, Venepally P, Wall A, Puskás LG, Barzó P, Steemers FJ, Schork NJ, Scheuermann RH, Lasken RS, Lein ES, Tamás G