The tempest in a cubic millimeter: Image-based refinements necessitate the reconstruction of 3D microvasculature from a large series of damaged alternately-stained histological sections

This work presents two methods that facilitate a 3D reconstruction of microscopic blood vessels in the volume slightly larger than 1 mm 3 . The source of the data are histological serial sections, i.e., microscopic images of probes, stained with immunohistochemistry. Odd and even sections have different stainings in our primary data set. Thus, firstly, an approach to register an alternately-stained series is presented. With image filtering and a feature-detection-based registration we obtain a registered stack of 148 serial sections. The series has missing sections, locally damaged sections, artifacts from acquisition. All these hinder correct connectivity of blood vessels. With our second approach we interpolate the missing information while maintaining the connectivity. We achieve this with deformations based on dense optical flow. The presented methodology is applicable to further histological series. A combination of both approaches allows us to reconstruct more than 76% larger volumes. An important detail was the composition mode of images. Summarizing, we use methods from image processing and computer vision to create large-scale 3D models from immunostained histological serial sections.