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Sunday, July 19 • 7:00pm - 8:00pm
P42: A nanometer range reconstruction of the Purkinje cell dendritic tree for computational models

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Mykola Medvidov, Weiliang Chen, Christin Puthur, Erik De Schutter

Purkinje neurons are used extensively in computational neuroscience [1]. However, despite extended knowledge about Purkinje cell morphology and ultrastructure, the complete dendritic tree of Purkinje cell as well as the complete dendritic tree of other types of neurons was never reconstructed at nanometer range resolution due to the cells size and complexity. At the same time, the use of real Purkinje cell dendritic tree morphology may be very important for computational models. Considering the development of new instruments and imaging techniques that nowadays allow reconstruction of large volumes of the neuronal tissue the main goal of our project is to reconstruct a dendritic tree of a Purkinje cell with all its dendritic spines and synapses.

Serial Block Face Microscope (SBF) is widely used to examine large volume of neuronal tissue with nanometer range resolution [2]. To obtain volume data perfused mouse brains were processed for SBF imaging using OTO staining techniques and the best quality cerebellum slice was imaged on FEI Teneo VS Electron Microscope with pixel resolution 8x8x60 nm. An imaged volume of approximately 2.2 Terapixel was processed and aligned with Image J and Adobe Photoshop. To reconstruct the Purkinje cell dendritic tree the imaged volume was first analyzed to locate the most appropriate full cell inside the imaged volume. Second, the volume containing the cell was segmented with Ilastik [https://www.ilastik.org](https://www.ilastik.org/) and Tensor Flow deep learning network https://github.com/tensorflow. The super-pixels were fused with custom made software to generate a dendritic tree represented by 3d voxels. Next, a 3d surface mesh was generated based on 3d voxels array using the marching cubes algorithm [https://github.com/ilastik/marching_cubes](https://github.com/ilastik/marching_cubes) and the resulting mesh was processed with MeshLab to generate a final surface mesh. Finally, a tetrahedral volume mesh was generated with the TetWild software [https://github.com/Yixin-Hu/TetWild](https://github.com/Yixin- Hu/TetWild). The resulting tetrahedral mesh of Purkinje cell full dendritic tree including cell body and initial axonal segment will be used to run large scale stochastic models using the parallel STochastic Engine for Pathway Simulation [3] (STEPS) http://steps.sourceforge.net.


1. Zang Y, Dieudonne S, De Schutter E. Voltage- and Branch-Specific Climbing Fiber Responses in Purkinje Cells. _Cell Reports_ 2018, 24, 1536–1549. 2. Titze B, Genoud C. Volume scanning electron microscopy for imaging biological ultrastructure. _Biology of the Cell_ 2016, 108, 307-323. 3. Chen W, De Schutter E. Parallel STEPS: Large Scale Stochastic Spatial Reaction-Diffusion Simulation with High Performance Computers. _Frontiers in Neuroinformatics_ 2017, 11, 1-15.


Mykola Medvidov

Computation Neuroscience Unit, Okinawa Institute of Science and Technology

Sunday July 19, 2020 7:00pm - 8:00pm CEST
Slot 17