Samples, Sources, Space: Decomposing Data Scale in Spatially Structured Representation Learning of Human Brain Microarchitecture

Christian Schiffer, Mathis Bode, Thomas Lippert, Katrin Amunts, Timo Dickscheid

Scaling studies typically represent training data by a single count of samples. For hierarchically and spatially structured data, however, the same number of samples can be drawn from few or many sources and distributed differently across the underlying domain. We therefore study data scaling as an allocation problem, separating unique sample count, source diversity, and spatial coverage. We study this decomposition in microscopic whole-brain histology, where a source is an individual brain, and a sample is an image patch at a specific spatial location. Across 93 controlled pretraining runs of a contrastive model that uses spatial proximity for supervision, we vary data allocation, compute, and model capacity over 11.6 million spatially anchored image patches from 21 human brains. Performance improves with more unique samples, broader spatial coverage, additional compute, and larger model capacity. At fixed sample count, distributing samples across one to 18 subjects produces no detectable improvement, even though representations generalize substantially better to subjects encountered during pretraining. Inter-subject variation therefore strongly affects generalization, but…