WHOLISTIC Lets Scientists Watch Cell Signaling Across a Living Zebrafish

Physiology is inherently multi-organ: neural activity, circulation, digestion and sensory responses can change together. Yet most live-imaging approaches observe only one tissue or one organ at a time. WHOLISTIC—short for WHole Organism Live Imaging System for recording Tissue and IntraCellular activity—was developed to address that gap in transparent young zebrafish. It combines fast 3D fluorescence imaging, genetically encoded calcium sensors and computational analysis to capture time-varying cellular activity across the body on second-scale timescales. 2

How WHOLISTIC works

The method begins with larval Danio rerio zebrafish, whose transparency makes internal tissues accessible to optical imaging. The animals express calcium sensors broadly across cells; changes in fluorescence provide a readout of intracellular calcium dynamics. Calcium activity is an informative proxy for cell-state changes, but it is not a direct measurement of synaptic connections or proof that one cell caused another to respond. 2

WHOLISTIC’s technical advance is an integrated workflow:

• Volumetric fluorescence microscopy repeatedly captures a three-dimensional view of the animal rather than a single imaging plane. 2
• Pan-cellular calcium labeling allows activity to be observed across cell types and organ systems, not only in neurons. 2
• Computational processing and machine learning help identify activity-bearing cellular structures and organize the large recordings into interpretable patterns. 2

Together, these components enable real-time recordings of cellular dynamics across the organism. The important shift is conceptual as well as technical: body-wide activity can be studied as a coordinated system, with candidate links between organs visible in the same experiment. 2

What whole-body imaging revealed

Low oxygen and blood-flow redirection

In low-oxygen conditions, WHOLISTIC revealed coordinated activity associated with changes in circulation, including a redirection of blood flow. Janelia’s WHOLISTIC gallery illustrates reduced blood flow in the mesenteric region during hypoxia, alongside increased flow toward the brain and heart. 8

This type of observation can connect neural and cardiovascular responses in a single preparation. It supports the idea that a coordinated body-wide response helps prioritize oxygen delivery to vital organs, while leaving the precise causal circuit to be tested with targeted follow-up experiments. 28

Spinal-cord dynamics and ependymal cells

The platform also identified coordinated dynamics in the spinal cord and in ependymal cells, which line the ventricular system. Those observations point to activity patterns that extend beyond conventional neuron-centered maps. 2

The finding is hypothesis-generating: state-linked ependymal activity may be relevant to sleep-associated physiology, but calcium correlations alone do not establish a sleep function. WHOLISTIC provides a way to identify such candidates across tissues and then test them with more selective perturbation experiments. 2

Ketamine effects across tissue boundaries

Drug responses can be distributed across multiple cell types and anatomical compartments. Using WHOLISTIC, researchers examined acute ketamine exposure and observed effects involving both neural tissue and the meninges. 2

That result illustrates the platform’s practical value: a measurement focused only on neurons could overlook responses in neighboring non-neural tissues. Whole-body imaging makes those tissue-boundary effects visible in the same experiment. 2

Cold-sensitive cartilage-associated cells

Cooling experiments also revealed calcium responses in cartilage-associated cells. The observation suggests that temperature-linked activity is not restricted to the nervous system and demonstrates how broad cellular imaging can uncover unexpected candidate sensory roles for non-neuronal tissues. 2

Why WHOLISTIC matters

WHOLISTIC extends the logic of zebrafish whole-brain imaging to the rest of the body. Whole-brain imaging in zebrafish had already shown that transparent vertebrates can support large-scale recordings of neural activity; the newer approach broadens the view to multiple organ systems and cell types simultaneously. 52

This matters for questions in which the relevant biology spans systems: how the brain coordinates circulation under stress, how medicines affect neural and non-neural tissues, or how sensory signals are represented outside traditional neural pathways. Rather than claiming a complete causal map, the method creates a body-wide activity map that can identify relationships worth testing. 2

An open and extensible imaging direction

Janelia presents the underlying work as a resource built around advanced microscopy and computational analysis, and its WHOLISTIC site includes visualizations of results such as hypoxia-linked circulation changes. 28

The approach may also be useful beyond larval zebrafish. Danionella is a particularly promising model because adults remain very small enough for whole-brain recording, enabling research on more developed behavioral repertoires. Separately, Janelia reports that its whole-body expansion-microscopy workflow works with mature Danionella samples. 114

The key caveat remains central: calcium imaging reveals correlated cellular dynamics. It does not by itself establish direct connectivity, identify every molecular mechanism or prove causality. WHOLISTIC’s strength is that it makes cross-organ hypotheses observable at a scale that was previously difficult to access in a living vertebrate. 2