Reconstructing the three-dimensional surface of a branching and merging biological structure from a stack of coplanar contours

Abstract

We address here two important problems when reconstructing the three-dimensional surface of a biological structure from a stack of section contours. The correspondence problem, which aims at associating contours on adjacent sections, is solved using connection constraints and a contour association cost function to build a correspondence graph. The branching problem, which aims to reconstruct the surface between one contour and several ones on the adjacent section, is decomposed as a cascade of bifurcations at linearly interpolated contour locations between sections. Our method restores connections even for distant contours and produces anatomically relevant branching reconstructions. The validity of this approach is illustrated on two neuroanatomical datasets.

Life Sentence: Mollusc Prisoner in Cretaceous Brachiopod Reconstructed in 3D. First Evidence for the Co-Existence of A Mollusc Inside a Living Animal

“…The number of images to be registered and segmented can become very large. Here, we took advantage of the 3D reconstruction and modelling software Free-D, initially developed for neuroanatomy then cell biology studies 26,27 to propose an alternative approach avoiding all these constraints. We show here how using Free-D allowed us to generate insightful 3D reconstructions from manual drawings of sections digitized at arbitrary and varying intervals.…”

“…During this process, branching structures were automatically detected and meshed. 27 More complex topological changes such as the transition from closed to open structures were processed by separately reconstructing parts with different topologies followed by stitching them at additional intermediate slices using a speci cally developed tool. The reconstructed 3D models were interactively displayed using the Free-D viewer.…”