Neural activity is not random but displays sparse, organized spatiotemporal patterns, even in the absence of structured external stimulation. Neuronal assemblies, defined as populations of neurons that are co-activated, have been proposed as fundamental units of computations underlying a wide variety of cognitive processes such as perception, memory and behavior. However, little is known about the biological relevance of these assemblies and whether they have a functional significance. We used confocal calcium imaging to record spontaneous activity in the zebrafish habenula and implemented a previously established PCA-based analysis pipeline to identify neuronal assemblies. We recorded from 18 larval zebrafish between 6-16 days post-fertilisation days old and observed repeated, temporally structured patterns of network activity in the habenula. Using this approach we began probing how assemblies change across early developmental stages and if they are shaped by experience dependent factors such as social isolation. Additionally, we explored how these assemblies are involved in threat detection in response to auditory and visual stimuli.