Possum—A Framework for Three-Dimensional Reconstruction of Brain Images from Serial Sections

Abstract

Techniques based on imaging serial sections of brain tissue provide insight into brain structure and function. However, to compare or combine them with results from three dimensional imaging methods, reconstruction into a volumetric form is required. Currently, there are no tools for performing such a task in a streamlined way. Here we propose the Possum volumetric reconstruction framework which provides a selection of 2D to 3D image reconstruction routines allowing one to build workflows tailored to one’s specific requirements. The main components include routines for reconstruction with or without using external reference and solutions for typical issues encountered during the reconstruction process, such as propagation of the registration errors due to distorted sections. We validate the implementation using synthetic datasets and actual experimental imaging data derived from publicly available resources. We also evaluate efficiency of a subset of the algorithms implemented. The Possum framework is distributed under MIT license and it provides researchers with a possibility of building reconstruction workflows from existing components, without the need for low-level implementation. As a consequence, it also facilitates sharing and data exchange between researchers and laboratories.

Topography of claustrum and insula projections to medial prefrontal and anterior cingulate cortices of the common marmoset (Callithrix jacchus)

“…Top row: Rostral, lateral, and schematic view of the marmoset claustrum reconstructed from Nissl-stained coronal sections using the POSSUM software package(Majka et al, 2015). The thick blue line in each view shows the foreshortening of the rostral sections in the lateral view of the reconstruction, which is reflected in the heat maps in later figures.…”

Towards a comprehensive atlas of cortical connections in a primate brain: Mapping tracer injection studies of the common marmoset into a reference digital template

“…The next step was to use the deformable reconstruction scheme (Adler et al, ; Majka and Wójcik, ) to account for uncorrelated, section‐specific distortions of the individual sections, i.e., small amounts of compression, stretching, and bending of the tissue. The deformable reconstruction method stems from an assumption that variability of the shape of the brain structures is larger (i.e., it extends further) than the section thickness itself, thus the neighboring images are similar to one another in a formal sense (Adler et al, ; Gaffling et al, ).…”

Towards a comprehensive atlas of cortical connections in a primate brain: Mapping tracer injection studies of the common marmoset into a reference digital template

“…The Possum reconstruction framework ( Majka and Wójcik, 2015 ; https://github.com/pmajka/poSSum) provided computational pipelines for individual sub-tasks in the reconstruction of series of two dimensional images into 3D form. Image registration was performed by the Advanced Normalization Tools (ANTS) software suite ( Klein et al, 2009 ;Avants et al, 2011 ; http://picsl.upenn.edu/software/ants/).…”

“…The next step was to use the deformable reconstruction scheme ( Adler et al, 2014 ;Majka and Wójcik, 2015 ) to account for uncorrelated, section specific distortions of the individual sections -i.e. small amounts of compression, stretching, and bending of the tissue.…”