WHOLISTIC: Recording Calcium Signals from Nearly Every Cell of a Whole Vertebrate

Key points

On September 9, 2026, a team at HHMI's Janelia Research Campus published WHOLISTIC in *Nature*: an imaging system that records, at cellular resolution and on second-scale timescales, the activity of nearly every cell of an entire vertebrate simultaneously — for the first time capturing what every cell in the cardiovascular, digestive, and nervous systems is "saying" while a zebrafish larva swims, feeds, and sleeps.

Background: from whole-brain to whole-body

Nearly all cells communicate using calcium ions — muscle contraction, synaptic firing, fertilization, and apoptosis all depend on it. Over a decade ago, the Ahrens lab and collaborators built methods for whole-brain calcium imaging in zebrafish larvae. The leap now is not sharper images but simultaneous, whole-body coverage: cell interactions across organs, cell types, and timescales could not previously be recorded all at once.

The four-part pipeline

1. Whole-cell transgenesis — getting nearly every cell to express a calcium sensor; the prerequisite for everything else. 2. High-speed volumetric imaging — no single microscope configuration fits all tissues and dynamic ranges. 3. Computation — aligning signals and identifying cell types by activity patterns. Many cell types show distinctive temporal activity signatures, enabling identification by behavior even without specific markers. 4. Whole-body expansion microscopy — physically enlarging tissue to reveal fine structure and cross-validate cell identities.

Work was done in zebrafish larvae with a proof-of-concept in adult *Danionella cerebrum*. Collaborators include UCL, Virginia Tech, and Tsinghua University.

First observations, by scale

• Cellular: cartilage cells respond to cold — counterintuitive, as chondrocytes are not classic cold-sensing cells; meninges (connective tissue around brain and spinal cord) respond to ketamine.
• Organ: rhythmic traveling waves along nephrons.
• Multi-organ: previously unknown muscle synergies and muscle–organ interactions.
• Whole-body: under hypoxia, the brainstem redistributes blood flow from the gut to the brain and muscle — a whole-body survival response previously only inferable.

Sleep clue

During prolonged locomotor rest, activity waves propagate along the spinal cord and brain, originating from ependymal cells lining the fluid-filled cavities of the CNS. This is a lead, not a conclusion; the role of ependymal cells in sleep awaits dedicated experiments.

Adding optogenetics

Combining optogenetics with WHOLISTIC enables all-optical brain–body causal dissection: activate a specific cell population with light while reading out the whole-body response — moving from correlation to causal testing.

Why it took a decade

• Sensor coverage: dozens of tissue-specific cell types, unlike the brain's neurons driven by shared promoters.
• Volumetric speed: second-to-subsecond calcium signals versus a whole-body volume, limited phototoxicity.
• Data volume: far beyond whole-brain; alignment, denoising, and segmentation all redesigned.
• Identity verification: solved via whole-body expansion microscopy.

Limitations

The method currently requires naturally transparent animals. Zebrafish larvae are transparent only for days; adult *Danionella* stays transparent but is tiny with a limited behavioral repertoire. Mammals are out of reach — scattering is a physical limit, not an engineering one, so imaging an entire human body remains far off.

Next steps and applications

The team is adapting the method to *Danionella cerebrum*, whose lifelong transparency and adult behaviors enable more complex whole-body coordination studies. Likely first beneficiaries:

1. Whole-body drug side effects — non-target tissue responses (e.g., cartilage responding to cold) were never previously recorded. 2. Sleep and rest-state mechanisms — if the ependymal cell lead holds. 3. Inter-organ compensation — brainstem-driven blood redistribution, familiar in critical care but previously only inferred.

Perspective

Misha Ahrens: knowing only the brain to understand behavior is like knowing only one department to understand a large corporation — key information flows between departments. "Evolution only cares whether the organism works; it doesn't care whether a decision happens in prefrontal cortex or in a connection between brainstem and bladder."

Virginie Ruetten: the work connects two fundamental scales — cell and organism — filling an "observability gap."

Verdict: WHOLISTIC is currently more methodologically significant than discovery-driven. The observations across four scales are real and interesting but each awaits mechanistic follow-up. Its true contribution is making simultaneous study of physiology, neuroscience, behavior, and cell biology in one animal routine.

References

1. phys.org, "A 'wholistic' view of cellular communication across an entire animal" (2026-09) — https://phys.org/news/2026-09-wholistic-view-cellular-communication-entire.html 2. Science Net China coverage of the Nature paper (2026-09-09) — https://paper.sciencenet.cn/htmlpaper/2026/9/2026911195311334155345.shtm 3. Times of India (2026-09) — https://timesofindia.indiatimes.com/science/discovery/scientists-built-a-system-that-watches-activity-across-nearly-every-cell-of-a-living-vertebrate-at-once 4. ScienceAlert / Chinese coverage (2026-09-12) — https://www.toutiao.com/article/7684531595373593134/ 5. Nature paper: Ruetten, Ahrens et al., WHOLISTIC whole-body in vivo imaging system, published online 2026-09-09