, Volume 15, Issue 1, pp 5–12 | Cite as

N3DFix: an Algorithm for Automatic Removal of Swelling Artifacts in Neuronal Reconstructions

  • Eduardo Conde-Sousa
  • Peter Szücs
  • Hanchuan Peng
  • Paulo Aguiar
Software Original Article


It is well established that not only electrophysiology but also morphology plays an important role in shaping the functional properties of neurons. In order to properly quantify morphological features it is first necessary to translate observational histological data into 3-dimensional geometric reconstructions of the neuronal structures. This reconstruction process, independently of being manual or (semi-)automatic, requires several preparation steps (e.g. histological processing) before data acquisition using specialized software. Unfortunately these processing steps likely produce artifacts which are then carried to the reconstruction, such as tissue shrinkage and formation of swellings. If not accounted for and corrected, these artifacts can change significantly the results from morphometric analysis and computer simulations. Here we present N3DFix, an open-source software which uses a correction algorithm to automatically find and fix swelling artifacts in neuronal reconstructions. N3DFix works as a post-processing tool and therefore can be used in either manual or (semi-)automatic reconstructions. The algorithm’s internal parameters have been defined using a “ground truth” dataset produced by a neuroanatomist, involving two complementary manual reconstruction procedures: in the first, neuronal topology was faithfully reconstructed, including all swelling artifacts; in the second procedure a meticulous correction of the artifacts was manually performed directly during neuronal tracing. The internal parameters of N3DFix were set to minimize the differences between manual amendments and the algorithm’s corrections. It is shown that the performance of N3DFix is comparable to careful manual correction of the swelling artifacts. To promote easy access and wide adoption, N3DFix is available in NEURON, Vaa3D and Py3DN.


Neuronal reconstruction Swelling artifacts Morphometric analysis Neuronal simulations Artifact removal algorithm 



This work was partially supported by FEDER - Fundo Europeu de Desenvolvimento Regional funds through the COMPETE 2020 - Operacional Programme for Competitiveness and Internationalisation (POCI), Portugal 2020, and by Portuguese funds through FCT - Fundação para a Ciência e a Tecnologia/ Ministério da Ciência, Tecnologia e Inovação in the framework of the project “Institute for Research and Innovation in Health Sciences” (POCI-01-0145-FEDER-007274). (ECS) was partially supported by CMUP (UID/MAT/00144/2013), which is funded by FCT (Portugal) with national (MEC) and European structural funds (FEDER), under the partnership agreement PT2020; and by the strategic programme UID/BIA/04050/2013 (POCI-01-0145-FEDER-007569) funded by national funds through the FCT I.P. and by the ERDF through the COMPETE2020 - Programa Operacional Competitividade e Internacionalização (POCI). (PSz) was partially supported by the KTIA_NAP_13-2-2014-0005 grant of the Hungarian Government, and the János Bolyai Research Scholarship of the Hungarian Academy of Sciences.

The work presented here received support and was potentiated by the BigNeuron hackathons (Peng, Hawrylycz et al. 2015). The authors would like to thank Xiaoxiao Liu and Zhi Zhou for help in the integration of N3DFix plugin in Vaa3D.


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Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  • Eduardo Conde-Sousa
    • 1
    • 2
    • 3
  • Peter Szücs
    • 4
    • 5
  • Hanchuan Peng
    • 6
  • Paulo Aguiar
    • 3
    • 7
    • 8
  1. 1.CBMA – Centre of Molecular and Environmental Biology, Department of BiologyUniversity of MinhoBragaPortugal
  2. 2.CIBIO-InBIO – Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do PortoVairãoPortugal
  3. 3.CMUP – Centro de MatemáticaUniversidade do PortoPortoPortugal
  4. 4.MTA-DE-NAP B-Pain Control Research GroupDebrecenHungary
  5. 5.Department of PhysiologyUniversity of DebrecenDebrecenHungary
  6. 6.Allen Institute for Brain ScienceSeattleUSA
  7. 7.i3S – Instituto de Investigação e Inovação em SaúdeUniversidade do PortoPortoPortugal
  8. 8.INEB – Instituto de Engenharia BiomédicaUniversidade do PortoPortoPortugal

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