Event Abstract

Three-dimensional reconstruction of brain images from serial sections using the Possum framework

  • 1 Nencki Institute of Experimental Biology, Poland

Techniques based on imaging serial sections of brain tissue provide insight into brain structure and function and the usage of complementary approaches is considered indispensable in characterizing the spatial organization of neuronal structures and their circuitry. However, to compare or combine them with results from three dimensional imaging methods, reconstruction into a volumetric form is required. To perform such tasks in a streamlined way we introduce the Possum framework [1], software for reconstruction of three-dimensional images of the brain from series of two-dimensional images of stained sections. To develop the framework we reviewed and selected workflows which accomplish versatile reconstruction tasks according to today’s best practices. Additionally, we demonstrate properties of individual routines and illustrate which reconstruction task they are suitable for, and evaluate the efficiency of a subset of the algorithms implemented. We also validate the implementation using synthetic datasets and actual experimental imaging data derived from publicly available resources [2]. Finally, we present actual computational pipelines created using the framework [3,4]. The framework 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. The source code is distributed under the terms of the MIT license and is available to download from the GitHub repository: https://github.com/pmajka/poSSum.


The work was supported by the European Regional Development Fund under the Operational Programme Innovative Economy, POIG.02.03.00-00-003/09.


[1] Majka P, Wójcik DK. 2015. Possum-A Framework for Three-Dimensional Reconstruction of Brain Images from Serial Sections. Neuroinformatics, doi: 10.1007/s12021-015-9286-1.

[2] Johnson GA, Badea A, Brandenburg J, Cofer G, Fubara B, Liu S, Nissanov J. 2010. Waxholm space: an image-based reference for coordinating mouse brain research. Neuroimage. 53:365–372.

[3] Majka P, Chaplin TA, Yu H-H, Tolpygo A, Mitra PP, Wójcik DK, Rosa MG. 2016. Towards a comprehensive atlas of cortical connections in a primate brain: Mapping tracer injection studies of the common marmoset into a reference digital template. J Comp Neurol. doi: 10.1002/cne.24023.

[4] Zakiewicz IM, Majka P, Wójcik DK, Bjaalie JG, Leergaard TB. 2015. Three-Dimensional Histology Volume Reconstruction of Axonal Tract Tracing Data: Exploring Topographical Organization in Subcortical Projections from Rat Barrel Cortex. PLoS One. 10:e0137571.

Keywords: 3D Reconstruction, Brain Atlas, Histology, image analysis, image registration, light microscopy

Conference: Neuroinformatics 2016, Reading, United Kingdom, 3 Sep - 4 Sep, 2016.

Presentation Type: Poster

Topic: Digital atlasing

Citation: Majka P and Wójcik DK (2016). Three-dimensional reconstruction of brain images from serial sections using the Possum framework. Front. Neuroinform. Conference Abstract: Neuroinformatics 2016. doi: 10.3389/conf.fninf.2016.20.00053

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Received: 02 May 2016; Published Online: 18 Jul 2016.

* Correspondence: Dr. Piotr Majka, Nencki Institute of Experimental Biology, Warsaw, Poland, p.majka@nencki.edu.pl