The anatomy of brain wiring is often taken as an established and permanent body of knowledge, sometimes considered as a 'ground truth', which supposedly provides a secure basis for validating structural and functional imaging data, for building neural network models, or for constraining inferences on causal mechanisms generating brain activity.

Macroscopical brain anatomy changes only slowly with ontogenetic development. Also, at any stage morphological data are less variable than most functional measurements. Nevertheless, there is considerable dynamics at the microscopical scale. Also, observer- and method-dependence determine which structural features are unanimously recognized and which others depend critically on sensitivity and specificity, or are inferred on the basis of pre-existing knowledge. Many structural features vary between species or within species or with plasticity and learning. There are also structural features that lack a known functional correlate, or where the structure and the function are not as tightly coupled as we would expect them to be. This variety of observations illustrates that it is important to know the circumstances and limitations of anatomical observations.

Here I present anatomical methods used for establishing structural connectivity in the brain and discuss some prerequisites that have to be fulfilled to ensure that the anatomical data on brain connectivity support the inferences that we like to base upon them.

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