, Volume 14, Issue 4, pp 369–385 | Cite as

Neuron-Miner: An Advanced Tool for Morphological Search and Retrieval in Neuroscientific Image Databases

  • Sailesh ConjetiEmail author
  • Sepideh Mesbah
  • Mohammadreza Negahdar
  • Philipp L. Rautenberg
  • Shaoting Zhang
  • Nassir Navab
  • Amin Katouzian
Original Article


The steadily growing amounts of digital neuroscientific data demands for a reliable, systematic, and computationally effective retrieval algorithm. In this paper, we present Neuron-Miner, which is a tool for fast and accurate reference-based retrieval within neuron image databases. The proposed algorithm is established upon hashing (search and retrieval) technique by employing multiple unsupervised random trees, collectively called as Hashing Forests (HF). The HF are trained to parse the neuromorphological space hierarchically and preserve the inherent neuron neighborhoods while encoding with compact binary codewords. We further introduce the inverse-coding formulation within HF to effectively mitigate pairwise neuron similarity comparisons, thus allowing scalability to massive databases with little additional time overhead. The proposed hashing tool has superior approximation of the true neuromorphological neighborhood with better retrieval and ranking performance in comparison to existing generalized hashing methods. This is exhaustively validated by quantifying the results over 31266 neuron reconstructions from dataset curated from 147 different archives. We envisage that finding and ranking similar neurons through reference-based querying via Neuron Miner would assist neuroscientists in objectively understanding the relationship between neuronal structure and function for applications in comparative anatomy or diagnosis.


Neuroscientific databases Data mining Hashing Neuromorphological space Random Forests 



We thank Ajayrama Kumaraswamy, Computational Neuroscience Department Biology II, Ludwigs Maximillian Universität München, Germany for insightful discussion in the early conception of this work. We thank the assistance of Bastien Saquet of Max Plank Digital Library, München, Germany in maintaining the web-service. We would like to thank the Max Plank Digital Library, München, Germany for providing computing resources for hosting the Neuron-Miner software and making it publicly accessible.

Conflict of interests

We have no conflict of interest to declare.

Supplementary material

(WMV 3.49 MB)


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Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  • Sailesh Conjeti
    • 1
    Email author
  • Sepideh Mesbah
    • 1
  • Mohammadreza Negahdar
    • 4
  • Philipp L. Rautenberg
    • 2
  • Shaoting Zhang
    • 3
  • Nassir Navab
    • 1
  • Amin Katouzian
    • 4
  1. 1.Chair for Computer Aided Medical ProceduresTechnische Universität MünchenMünchenGermany
  2. 2.Max Plank Digital LibraryMünchenGermany
  3. 3.Department of Computer ScienceUniversity of North Carolina at CharlotteCharlotteUSA
  4. 4.IBM Almaden Research CenterCAUSA

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