SpineLab: Tool for three-dimensional reconstruction of neuronal cell morphology

Daniel Jungblut, Andreas Vlachos, Gerlind Schuldt, Nadine Zahn, Thomas Deller, Gabriel Wittum*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

14 Scopus citations


SpineLab is a software tool developed for reconstructing neuronal feature skeletons from three-dimensional single-or multi-photon image stacks. These images often suffer from limited resolution and a low signal-to-noise ratio, making the extraction of morphometric information difficult. To overcome this limitation, we have developed a software tool that offers the possibility to create feature skeletons in various modes-automatically as well as with manual interaction. We have named this novel tool SpineLab. In a first step, an investigator adjusts a set of parameters for automatic analysis in an interactive manner, i.e., with online visual feedback, followed by a second step, in which the neuronal feature skeleton can be modified by hand. We validate the ability of SpineLab to reconstruct the entire dendritic tree of identified GFP-expressing neurons and evaluate the accuracy of dendritic spine detection. We report that SpineLab is capable of significantly facilitating the reconstruction of dendrites and spines. Moreover, the automatic approach appears sufficient to detect spine density changes in time-lapse imaging experiments. Taken together, we conclude that SpineLab is an ideal software tool for partially automatic reconstruction of neural cell morphology.

Original languageEnglish (US)
Article number076007
JournalJournal of biomedical optics
Issue number7
StatePublished - Jul 2012
Externally publishedYes

Bibliographical note

Funding Information:
We thank Sergei Wolf from G-CSC Frankfurt for creating the model neurons with NeuGen. The work was supported by a German-Israeli Foundation Grant (GIF G-2239-2096.1/2009), by Deutsche Forschungsgemeinschaft DFG (DE551/10-1;11-1), by BMBF via Bernstein-Group DMSPiN and by Baden-Württemberg-Stiftung via project HPC-12.


  • Dendritic tree
  • Graphical user interface
  • Morphology reconstruction
  • Neuronal feature skeleton
  • Neurons
  • Spine density changes
  • SpineLab-software
  • Spines

ASJC Scopus subject areas

  • Electronic, Optical and Magnetic Materials
  • Biomaterials
  • Atomic and Molecular Physics, and Optics
  • Biomedical Engineering


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