Keeler et al. 2022 · Van Deusen et al. 2025
Atlas Landscapes
Two single-cell mass cytometry atlases from the Deppmann and Zunder labs, redrawn as explorable 3D landscapes. Pick a cell state to see the proteins that define it and trace its route back to a common progenitor.
How to read a landscape
Waddington drew development as a ball rolling downhill into branching valleys. Here each valley ends in a marker-defined cell state from one of these atlases. Solid routes follow the published inferred trajectories or summary relationships. Dashed connections show earlier ancestry, alignment between analyses, or a putative state. Height and basin size are illustrative.
The routes are inferred from protein profiles across ages, and none of them is a lineage trace. The developmental-time scrubber is a source-qualified preview: sensory ages come from published phenotype windows, and brain ages from the sampled root and tip populations. States without a mapped age appear as age unassigned: we have no date for them yet, so a dimmed branch says nothing about whether those cells exist at the selected stage.
Each model is about 5 MB and loads only when you choose Explore in 3D. Every state and connection is also listed in a plain-text version.
Sensory atlas · E11.5–P4
The developing sensory system
Fourteen neuronal outcomes and seven glial outcomes connect to an earlier neural crest progenitor. Explore the marker-defined states underlying touch, body position, and other somatosensory functions.
Select an outcome to see its common name, marker profile, and source. The transition explorer follows the route back to the common progenitor.
The shared neural crest ancestor predates the sampled common-root interval. Dashed links mark earlier ancestry or a putative state. The terrain is a conceptual Waddington landscape: height, width, and basin area are illustrative. The branches summarize published inferred trajectories and developmental relationships.
Developing brain atlas · E11.5–P4
The developing brain
Twenty-two analysis tips and four supplementary nonneural profiles span neuronal, glial, and other cellular states. The two neural analyses overlap; their tips are displayed as separate analytical views.
Compare marker-defined precursors and end states, then inspect each connection. Some analysis tips retain progenitor identities or uncertain functional assignments.
The early epiblast summit provides inferred developmental context for neural and nonneural profiles. The brain CyTOF paper did not reconstruct those upstream links. Dashed connections also identify alignment between overlapping analyses. No branch represents direct lineage tracing; mountain dimensions are illustrative.
Sources
Both atlases are joint work of the Deppmann lab and Eli Zunder's lab at the University of Virginia.
- Keeler et al., 2022. A developmental atlas of somatosensory diversification and maturation in the dorsal root ganglia by single-cell mass cytometry. Nature Neuroscience.
- Van Deusen et al., 2025. A single-cell mass cytometry-based atlas of the developing mouse brain. Nature Neuroscience.
- The brain landscape's epiblast summit draws on external developmental context: Pijuan-Sala et al., 2019. A single-cell molecular map of mouse gastrulation and early organogenesis. Nature.
These visualizations were built from the papers' published figures and annotations, without reanalyzing the raw mass cytometry data. For measured single-cell signaling responses, see the BDNF Signaling Atlas.