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3dSpAn: An interactive software for 3D segmentation and analysis of dendritic spines

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Abstract

Three-dimensional segmentation and analysis of dendritic spine morphology involve two major challenges: 1) how to segment individual spines from the dendrites and 2) how to quantitatively assess the morphology of individual spines. To address these two issues, we developed software called 3dSpAn (3-dimensional Spine Analysis), based on implementing a previously published method, 3D multi-scale opening algorithm in shared intensity space. 3dSpAn consists of four modules: a) Preprocessing and Region of Interest (ROI) selection, b) Intensity thresholding and seed selection, c) Multi-scale segmentation, and d) Quantitative morphological feature extraction. In this article, we present the results of segmentation and morphological analysis for different observation methods and conditions, including in vitro and ex vivo imaging with confocal microscopy, and in vivo observations using high-resolution two-photon microscopy. In particular, we focus on software usage, the influence of adjustable parameters on the obtained results, user reproducibility, accuracy analysis, and also include a qualitative comparison with a commercial benchmark. 3dSpAn software is freely available for non-commercial use at www.3dSpAn.org.

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Acknowledgements

This project was supported by the Department of Biotechnology, India grant: BT/PR16356/BID/7/596/2016 (S.B) and the Polish National Science Centre, grant 2017/26/E/NZ4/00637 (J.W.). N.D. acknowledges CSIR SRF Fellowship, File No. 09|096(0921)2K18 EMR-I), India. E.B. acknowledges Polish National Science Centre grant UMO-2017/27/N/NZ3/02417. M.B. acknowledges Foundation for Polish Science grant POIR.04.04.00-00-43BC/17-00. D.P. has been supported by Polish National Science Centre (2019/35/O/ST6/02484, 2020/37/B/NZ2/03757), Foundation for Polish Science co-financed by the European Union under the European Regional Development Fund (TEAM to DP). The research was co-funded by Warsaw University of Technology within the Excellence Initiative: Research University (IDUB) programme. We would like to thank Anthony Woodley for English language corrections.

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Author notes

  1. Nirmal Das and Ewa Baczynska are joint first authors, and they have contributed equally to this work.

Authors and Affiliations

  1. Department of CSE, Jadavpur University, 188 Raja S.C. Mullick Road, Kolkata, 700032, India

    Nirmal Das & Subhadip Basu

  2. Department of CSE, School of Engineering and Technology, Adamas University, Barbaria, Kolkata, West Bengal, 700126, India

    Nirmal Das

  3. Laboratory of Cell Biophysics, The Nencki Institute of Experimental Biology, Polish Academy of Sciences, Pasteura 3, 02-093, Warsaw, Poland

    Ewa Baczynska, Monika Bijata & Jakub Wlodarczyk

  4. The Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzak Street 44/52, 01-22, Warsaw, Poland

    Ewa Baczynska

  5. Laboratory of Bioinformatics and Computational Genomics, Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland

    Dariusz Plewczynski

  6. Laboratory of Functional and Structural Genomics, Centre of New Technologies, University of Warsaw, Warsaw, Poland

    Dariusz Plewczynski

  7. Department of Electrical and Computer Engineering & Department of Radiology, University of Iowa, Iowa City, IA 52242, USA

    Punam Kumar Saha

  8. Cellular Neurophysiology, Hannover Medical School, 1 Carl-Neuberg Street, Hannover, 30625, Germany

    Andre Zeug & Evgeni Ponimaskin

  9. Laboratory of Imaging Tissue Structure and Function, The Nencki Institute of Experimental Biology, Polish Academy of Sciences, Pasteura 3, 02-093, Warsaw, Poland

    Blazej Ruszczycki

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Contributions

S.B. and J.W. conceived the study; S.B., P.K.S., D.P., J.W. performed the experimental design; N.D., S.B. developed the software; N.D., E.B., M.B., A.Z., B.R. analyzed the data; S.B., N.D., B.R, E.B., J.W, E.P., M.B. wrote the manuscript.

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Correspondence to Jakub Wlodarczyk or Subhadip Basu.

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Das, N., Baczynska, E., Bijata, M. et al. 3dSpAn: An interactive software for 3D segmentation and analysis of dendritic spines. Neuroinform 20, 679–698 (2022). https://doi.org/10.1007/s12021-021-09549-0

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