Neurovascular Network Explorer 2.0: A Simple Tool for Exploring and Sharing a Database of Optogenetically-evoked Vasomotion in Mouse Cortex In Vivo

Hana Uhlirova; Peifang Tian; Kıvılcım Kılıç; Martin Thunemann; Vishnu B. Sridhar; Radim Chmelik; Hauke Bartsch; Anders M. Dale; Anna Devor; Payam A. Saisan

doi:10.3791/57214

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Method Article

Neurovascular Network Explorer 2.0: A Simple Tool for Exploring and Sharing a Database of Optogenetically-evoked Vasomotion in Mouse Cortex In Vivo

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DOI:

10.3791/57214

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May 4th, 2018

Hana Uhlirova¹^,² , Peifang Tian³^,⁴ , Kıvılcım Kılıç³^,⁵ , Martin Thunemann¹ , Vishnu B. Sridhar⁶ , Radim Chmelik²^,⁷ , Hauke Bartsch¹ , Anders M. Dale¹^,³ , Anna Devor¹^,³^,⁸ , Payam A. Saisan³

¹Department of Radiology, University of California, San Diego, ²Central European Institute of Technology, Brno University of Technology, ³Department of Neurosciences, University of California, San Diego, ⁴Department of Physics, John Carroll University, ⁵Department of Biomedical Engineering, Boston University, ⁶Bioengineering Undergraduate Program, University of California, San Diego, ⁷Institute of Physical Engineering, Faculty of Mechanical Engineering, Brno University of Technology, ⁸Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard Medical School

Summary

A graphical user interface for exploring and sharing a database of optogenetically-induced vascular responses in mouse somatosensory cortex in vivo measured by 2-photon microscopy is presented. It allows browsing the data, criteria-based selection, averaging, localization of measurements within a 3D volume of vasculature and exporting the data.

Abstract

The importance of sharing experimental data in neuroscience grows with the amount and complexity of data acquired and various techniques used to obtain and process these data. However, the majority of experimental data, especially from individual studies of regular-sized laboratories never reach wider research community. A graphical user interface (GUI) engine called Neurovascular Network Explorer 2.0 (NNE 2.0) has been created as a tool for simple and low-cost sharing and exploring of vascular imaging data. NNE 2.0 interacts with a database containing optogenetically-evoked dilation/constriction time-courses of individual vessels measured in mice somatosensory cortex in vivo by 2-photon microscopy. NNE 2.0 enables selection and display of the time-courses based on different criteria (subject, branching order, cortical depth, vessel diameter, arteriolar tree) as well as simple mathematical manipulation (e.g. averaging, peak-normalization) and data export. It supports visualization of the vascular network in 3D and enables localization of the individual functional vessel diameter measurements within vascular trees.

NNE 2.0, its source code, and the corresponding database are freely downloadable from UCSD Neurovascular Imaging Laboratory website¹. The source code can be utilized by the users to explore the associated database or as a template for databasing and sharing their own experimental results provided the appropriate format.

Introduction

The brain is considered one of the most intricate organs and the desire to untangle its complex function is unflagging. It is being studied at different scales from the molecular to the behavioral level using a wide palette of tools²^,³^,⁴^,⁵^,⁶^,⁷^,⁸. The amount of non-homogeneous experimental data grows with unprecedented speed. The awareness of the need for experimental data sharing, organization and standardization grows with the amount of ....