Name: neurovascular network explorer 2.0: a simple tool for exploring and sharing a database of optogenetically-evoked vasomotion in mouse cortex in vivo
Uploaded: 2018-05-04T13:00:00
Description: Watch this Scientific Journal Video about Neurovascular Network Explorer 2.0: A Simple Tool for Exploring and Sharing a Database of Optogenetically-evoked Vasomotion in Mouse Cortex In Vivo at JoVE.co

We gratefully acknowledge support from the NIH (NS057198, EB00790, MH111359, and S10RR029050) and the Ministry of Education, Youth and Sports of the Czech Republic (CEITEC 2020, LQ1601). KK was supported by postdoctoral fellowships from the International Headache Society in 2014 and The Scientific and Technological Research Council of Turkey in 2015. MT was supported by postdoctoral fellowship from the German Research Foundation (DFG TH 2031/1).

1. Installation of NNE 2.0
<ol>
	<li>Go to UCSD Neurovascular Imaging Laboratory website1 and left-click at &#8216;NNE 2.0 HDbase v1.0&#8217; to download the zipped program files to the desired location on your PC. 
	NOTE: NNE 2.0 requires a Windows-operating system of versions 7-10, at least 2.8 GB of free space to download the zipped file and 6.9 GB to install the program.</li>
	<li>Unzip &#8216;NNE2_HDbase_v1.0.zip&#8217;. 
	NOTE: The unzipped folder NNE2 contains 10 files: &#8216;h...

<ol>
	<li>. Use Our Data Available from: <a target="_blank" href="https://neurosciences.ucsd.edu/research/labs/nil/Pages/UseOurData.aspx">https://neurosciences.ucsd.edu/research/labs/nil/Pages/UseOurData.aspx</a> (2017)</li><li>Craddock, R. C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Imaging+human+connectomes+at+the+macroscale.">Imaging human connectomes at the macroscale.</a> Nat Methods. 10 (6), 524-539 (2013).</li><li>Devor, A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Frontiers+in+optical+imaging+of+cerebral+blood+flow+and+metabolism.">Frontiers in optical imaging of cerebral blood flow and metabolism.</a> J Cereb Blood Flow Metab. 32 (7), 1259-1276 (2012).</li><li>Ji, N., Freeman, J., Smith, S. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Technologies+for+imaging+neural+activity+in+large+volumes.">Technologies for imaging neural activity in large volumes.</a> Nat Neurosci. 19 (9), 1154-1164 (2016).</li><li>Maze, I., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Analytical+tools+and+current+challenges+in+the+modern+era+of+neuroepigenomics.">Analytical tools and current challenges in the modern era of neuroepigenomics.</a> Nat Neurosci. 17 (11), 1476-1490 (2014).</li><li>Medland, S. E., Jahanshad, N., Neale, B. M., Thompson, P. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Whole-genome+analyses+of+whole-brain+data:+working+within+an+expanded+search+space.">Whole-genome analyses of whole-brain data: working within an expanded search space.</a> Nat Neurosci. 17 (6), 791-800 (2014).</li><li>Osten, P., Margrie, T. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mapping+brain+circuitry+with+a+light+microscope.">Mapping brain circuitry with a light microscope.</a> Nat Methods. 10 (6), 515-523 (2013).</li><li>Poldrack, R. A., Farah, M. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Progress+and+challenges+in+probing+the+human+brain.">Progress and challenges in probing the human brain.</a> Nature. 526 (7573), 371-379 (2015).</li><li>Kotter, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Neuroscience+databases:+tools+for+exploring+brain+structure-function+relationships.">Neuroscience databases: tools for exploring brain structure-function relationships.</a> Philos Trans R Soc Lond B Biol Sci. 356 (1412), 1111-1120 (2001).</li><li>Uhlirova, H., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+roadmap+for+estimation+of+cell-type-specific+neuronal+activity+from+non-invasive+measurements.">The roadmap for estimation of cell-type-specific neuronal activity from non-invasive measurements.</a> Philos Trans R Soc Lond B Biol Sci. 371 (1705), (2016).</li><li>Aine, C. J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Multimodal+Neuroimaging+in+Schizophrenia:+Description+and+Dissemination.">Multimodal Neuroimaging in Schizophrenia: Description and Dissemination.</a> Neuroinformatics. , (2017).</li><li>Amunts, K., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=BigBrain:+an+ultrahigh-resolution+3D+human+brain+model.">BigBrain: an ultrahigh-resolution 3D human brain model.</a> Science. 340 (6139), 1472-1475 (2013).</li><li>Laird, A. R., Lancaster, J. L., Fox, P. T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=BrainMap:+the+social+evolution+of+a+human+brain+mapping+database.">BrainMap: the social evolution of a human brain mapping database.</a> Neuroinformatics. 3 (1), 65-78 (2005).</li><li>Lein, E. S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Genome-wide+atlas+of+gene+expression+in+the+adult+mouse+brain.">Genome-wide atlas of gene expression in the adult mouse brain.</a> Nature. 445 (7124), 168-176 (2007).</li><li>Shin, D. D., Ozyurt, I. B., Liu, T. T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+Cerebral+Blood+Flow+Biomedical+Informatics+Research+Network+(CBFBIRN)+database+and+analysis+pipeline+for+arterial+spin+labeling+MRI+data.">The Cerebral Blood Flow Biomedical Informatics Research Network (CBFBIRN) database and analysis pipeline for arterial spin labeling MRI data.</a> Front Neuroinform. 7, 21 (2013).</li><li>Uhlirova, H., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Neurovascular+Network+Explorer+2.0:+A+Database+of+2-Photon+Single-Vessel+Diameter+Measurements+from+Mouse+SI+Cortex+in+Response+To+Optogenetic+Stimulation.">Neurovascular Network Explorer 2.0: A Database of 2-Photon Single-Vessel Diameter Measurements from Mouse SI Cortex in Response To Optogenetic Stimulation.</a> Front Neuroinform. 11, 4 (2017).</li><li>Sridhar, V. B., Tian, P., Dale, A. M., Devor, A., Saisan, P. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Neurovascular+Network+Explorer+1.0:+a+database+of+2-photon+single-vessel+diameter+measurements+with+MATLAB((R))+graphical+user+interface.">Neurovascular Network Explorer 1.0: a database of 2-photon single-vessel diameter measurements with MATLAB((R)) graphical user interface.</a> Front Neuroinform. 8, 56 (2014).</li><li>Tian, P., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cortical+depth-specific+microvascular+dilation+underlies+laminar+differences+in+blood+oxygenation+level-dependent+functional+MRI+signal.">Cortical depth-specific microvascular dilation underlies laminar differences in blood oxygenation level-dependent functional MRI signal.</a> Proc Natl Acad Sci U S A. 107 (34), 15246-15251 (2010).</li><li>. Use Our Data Available from: <a target="_blank" href="https://neurosciences.ucsd.edu/research/labs/nil/Pages/UseOurData.aspx">https://neurosciences.ucsd.edu/research/labs/nil/Pages/UseOurData.aspx</a> (2017)</li><li>Uhlirova, H., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cell+type+specificity+of+neurovascular+coupling+in+cerebral+cortex.">Cell type specificity of neurovascular coupling in cerebral cortex.</a> Elife. 5, (2016).</li><li>Gagnon, L., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Quantifying+the+microvascular+origin+of+BOLD-fMRI+from+first+principles+with+two-photon+microscopy+and+an+oxygen-sensitive+nanoprobe.">Quantifying the microvascular origin of BOLD-fMRI from first principles with two-photon microscopy and an oxygen-sensitive nanoprobe.</a> J Neurosci. 35 (8), 3663-3675 (2015).</li><li>Sakadzic, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Two-photon+high-resolution+measurement+of+partial+pressure+of+oxygen+in+cerebral+vasculature+and+tissue.">Two-photon high-resolution measurement of partial pressure of oxygen in cerebral vasculature and tissue.</a> Nat Methods. 7 (9), 755-759 (2010).</li><li>Nizar, K., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=In+vivo+stimulus-induced+vasodilation+occurs+without+IP3+receptor+activation+and+may+precede+astrocytic+calcium+increase.">In vivo stimulus-induced vasodilation occurs without IP3 receptor activation and may precede astrocytic calcium increase.</a> J Neurosci. 33 (19), 8411-8422 (2013).</li><li>Reznichenko, L., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=In+vivo+alterations+in+calcium+buffering+capacity+in+transgenic+mouse+model+of+synucleinopathy.">In vivo alterations in calcium buffering capacity in transgenic mouse model of synucleinopathy.</a> J Neurosci. 32 (29), 9992-9998 (2012).</li><li>Langer, J., Rose, C. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Synaptically+induced+sodium+signals+in+hippocampal+astrocytes+in+situ.">Synaptically induced sodium signals in hippocampal astrocytes in situ.</a> J Physiol. 587 (Pt 24), 5859-5877 (2009).</li><li>Gong, Y., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=High-speed+recording+of+neural+spikes+in+awake+mice+and+flies+with+a+fluorescent+voltage+sensor.">High-speed recording of neural spikes in awake mice and flies with a fluorescent voltage sensor.</a> Science. 350 (6266), 1361-1366 (2015).</li><li>Tantama, M., Hung, Y. P., Yellen, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Optogenetic+reporters:+Fluorescent+protein-based+genetically+encoded+indicators+of+signaling+and+metabolism+in+the+brain.">Optogenetic reporters: Fluorescent protein-based genetically encoded indicators of signaling and metabolism in the brain.</a> Prog Brain Res. 196, 235-263 (2012).</li><li>Devor, A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term="Overshoot"+of+O(2)+is+required+to+maintain+baseline+tissue+oxygenation+at+locations+distal+to+blood+vessels.">"Overshoot" of O(2) is required to maintain baseline tissue oxygenation at locations distal to blood vessels.</a> J Neurosci. 31 (38), 13676-13681 (2011).</li><li>Devor, A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Stimulus-induced+changes+in+blood+flow+and+2-deoxyglucose+uptake+dissociate+in+ipsilateral+somatosensory+cortex.">Stimulus-induced changes in blood flow and 2-deoxyglucose uptake dissociate in ipsilateral somatosensory cortex.</a> J Neurosci. 28 (53), 14347-14357 (2008).</li><li>Rauch, A., Rainer, G., Logothetis, N. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+effect+of+a+serotonin-induced+dissociation+between+spiking+and+perisynaptic+activity+on+BOLD+functional+MRI.">The effect of a serotonin-induced dissociation between spiking and perisynaptic activity on BOLD functional MRI.</a> Proc Natl Acad Sci U S A. 105 (18), 6759-6764 (2008).</li><li>Lemmon, V. P., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Minimum+information+about+a+spinal+cord+injury+experiment:+a+proposed+reporting+standard+for+spinal+cord+injury+experiments.">Minimum information about a spinal cord injury experiment: a proposed reporting standard for spinal cord injury experiments.</a> J Neurotrauma. 31 (15), 1354-1361 (2014).</li><li>Ascoli, G. A., Donohue, D. E., Halavi, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=NeuroMorpho.Org:+a+central+resource+for+neuronal+morphologies.">NeuroMorpho.Org: a central resource for neuronal morphologies.</a> J Neurosci. 27 (35), 9247-9251 (2007).</li><li>Mennes, M., Biswal, B. B., Castellanos, F. X., Milham, M. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Making+data+sharing+work:+the+FCP/INDI+experience.">Making data sharing work: the FCP/INDI experience.</a> Neuroimage. 82, 683-691 (2013).</li><li>Marmarou, A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=IMPACT+database+of+traumatic+brain+injury:+design+and+description.">IMPACT database of traumatic brain injury: design and description.</a> J Neurotrauma. 24 (2), 239-250 (2007).</li></ol>

NNE 2.0 was written in order to share the vascular imaging data of a specific study20 but with the intention of developing a simple tool for sharing and exploring data of similar kind by other users. Researchers interested in inspecting the associated database of vascular data may use the GUI to browse the data, select subsets of data, compare them to their own experimental results or process them further using their own computational procedures. Users familiar with MATLAB can utilize directly the...

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 acquired data. It has become evident that neuroinformatics will play a critical role in integrating experimental data across scales into models of brain function and dysfunction9,10.
To this end some studies, especially larger-scale studies, were able to earmark resources to make their results available via extensive databases11,12,13,14,15. However, a vast amount of experimental data from individual studies and regular-sized laboratories never reached the wider research community. This is mainly for two reasons: first, more dedicated time is needed to build a database and create tools that would enable the user to interact with the database; and second, more money is needed to support these tasks. Motivated by these challenges, a MATLAB based graphical user interface (GUI) engine called the Neurovascular Network Explorer 2.0 (NNE 2.0)16 was developed as a simple and low-cost tool for databasing, sharing and exploring of vascular imaging data. This manuscript provides a manual for operation of NNE 2.0 and the associated database of experimental data.
NNE 2.0 is already a second-generation software engine. The first generation, called Neurovascular Network Explorer 1.0 (NNE 1.0)17 was built to interact with a database of sensory-evoked vasodilation in rat primary somatosensory cortex (SI) in vivo measured by 2-photon microscopy18. NNE 1.0, its source code as well as the associated database are freely downloadable as a zipped file called &#8216;NNE 1 Tian&#8217; from UCSD Neurovascular Imaging Laboratory website1. More information about NNE 1.0 and the associated database can be found in17.
The second generation, the NNE 2.0, interacts with a database of optogenetically-evoked dilation of individual vessels in mice SI in vivo measured by 2-photon microscopy20. The user can browse, select and visualize data based on selection categories such as cortical depth, branching order, vessel diameter, animal subject or a particular arteriolar tree. The GUI further performs simple mathematical operations such as averaging and peak-normalization in selected categories. NNE 2.0 enables to view and browse through images capturing 3D volumes of vasculature as well as identify the location of the functional measurement within the vascular trees. This feature can be used to reconstruct vascular morphologies in 3D and populate them with real single-vessel vaso-motion measurements. These reconstructions can in turn be incorporated into computational models of brain function21,22. NNE 2.0, its source code and the associated database are freely downloadable as a zipped file called &#8216;NNE 2.0 HDbase v1.0&#8217; from UCSD Neurovascular Imaging Laboratory website1.
NNE 2.0 works with a database called &#39;vdb.mat&#39;. This database is a matrix containing temporal profiles (time-courses) of single vessel diameter changes evoked by an optogenetic stimulus and measured at different locations of arteriolar trees. Each time-course was computed using custom-written software. It calculates the relative change of a vessel diameter from expansion of a fluorescent intensity profile acquired by scanning across the vessel. The fluorescent contrast was presented by intravascular injection of fluorescein isothiocyanate (FITC)-labeled dextran. For more information about the data and analysis procedures, please see20,23. The database has 305 time-courses (i.e. database entries) in total. In addition to the diameter change, each entry to the database holds an array of additional metadata which (1) quantify the time-course (2) describe the measured vessel and (3) identify the measurement location within a 3D volume of cortical vasculature. The metadata include the onset time, peak amplitude, peak amplitude time, cortical depth, branching order, vessel diameter at baseline, path to original reference images and 3D image stacks for each measurement and low-magnification maps of brain surface vasculature. Please see all parameters in the metadata listed and described in detail previously in Table 116.
NNE 2.0 interacts with reference images that are X-Y scans of a plane where the diameter measurement occurred. Each database entry has one corresponding reference image with a reference name displayed in the GUI. Each database entry also has an associated stack of images (3D stack) capturing a 3D volume of the vascular tree within which the measurement occurred. The GUI enables to choose a particular database entry and display the corresponding reference image as well as the 3D stack. It also guides the user to find the matching reference image and frame in the 3D stack (the same features can be found in both images). All stack and reference images in their full resolution (1024 pix x 1024 pix) are included in folders hana_stk and hana_refs, respectively. Low-magnification maps of brain vasculature are included in folder &#39;maps&#39;. All three folders as well as the database matrix &#8216;vdb.mat&#8217; are downloaded in the zipped file &#8216;NNE 2.0 HDbase v1.0&#8217; from the UCSD Neurovascular Imaging Laboratory website1 and saved to the root folder of NNE 2.0 during the installation process.
The GUI has been designed as a set of four panels (Panel 1 (Main Panel) &#8211; Panel 4) which open sequentially as the user explores the database and selects specific data based on selection categories. Each panel is divided into two main parts: (1) the right column provides the possibility to interact with the database by selecting parameters and categories of the data and displays important information from the metadata; (2) the left column displays the data in the form of time-courses (diameter change in time) and scatter-plots. There are four types of scatter plots displaying (1) dilation onset time (2) time of the dilation peak (3) maximum diameter change (peak amplitude) and (4) baseline diameter (diameter before stimulation) as function of cortical depth. The user has the possibility to display average time-courses and values for selected data grouped either by cortical depth or branching order. This is to highlight the feature of gradient diameter-change behavior with increasing depth and branching order20. NNE 2.0 allows the user to export the selected subset of data in the format of &#39;.xls&#39;, &#39;.csv&#39; or &#39;.mat&#39;.

<table border="0" cellpadding="0" cellspacing="0" width="849">
	<tbody>
		<tr height="40">
			<td height="40" style="height:40px;width:216px;">MATLAB</td>
			<td style="width:123px;">MathWorks</td>
			<td style="width:344px;"></td>
			<td style="width:167px;">program</td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">Winrar</td>
			<td>Rarlabs</td>
			<td></td>
			<td>program</td>
		</tr>
	</tbody>
</table>

neurovascular network explorer 2.0: a simple tool for exploring and sharing a database of optogenetically-evoked vasomotion in mouse cortex in vivo

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.

NNE 2.0 and the associate database serve to browse and view the data of the database, sort out the data based on selection criteria, download the selected data, and find the vascular measurements within the corresponding vascular tree.
Panel 1 features selection of data based on categories: &#39;Cortical Depth&#39;, &#39;Branching Order&#39;, &#39;Baseline Diameter&#39; and &#39;Subjects&#39; &#8211; Figure ...

Watch this Scientific Journal Video about Neurovascular Network Explorer 2.0: A Simple Tool for Exploring and Sharing a Database of Optogenetically-evoked Vasomotion in Mouse Cortex In Vivo at JoVE.co

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

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.

The importance of sharing experimental data in neuroscience grows with the amount and complexity of data acquired and various techniques used to obtain ...

The presented software called Neurovascular Network Explorer 2.0 or NNE 2.0, is a MATLAB based graphical user interface which allows visualization, inspection, selection, and export of optogenetically-evoked vascular diameter changes measured by two photon microscopy. In any two supports localization of the diameter measurements within a 3D structure of vascular network which can be used in modern studies of brain function. And any two can be used to explore the associated database as well as a template to sharing and exploring users own data structured into database of similar format.Start the NNE 2.0 program by selecting NNE 2.execute. Images in the left column of the main panel show graphs of time courses and perimeters of all entries in the database vdb. mat Begin by selecting the range for cortical depth in the right column.A minimum depth of 40 microns and a maximum depth of 560 microns is used here. Then select branching order, left-click on the arrow and choose one of the options from the list shown. Next, select baseline diameter and type in the range.A minimum diameter of two microns and a maximum diameter of 45 microns is used here. Now, select the subjects to be analyzed in the right column of the panel. Left-click on the arrow and choose from the available options.Press submit to display and explore the selected data in panel two. Prior to exploring the selected subset of data, group average the data by left-clicking either average by cortical depth or average by branching order. The choice is highlighted in green below.Then select data based on vessel morphology or subject. Select all data for tree consists of the data for a single diving arterial and its branches. Next, left-click on submit to display selected data in graphs of individual time courses, group average time courses, and scatter plots of onset times, time-to-peak's peak amplitudes, and baseline diameters.Left-click on a trace in the graph of individual time courses. The selected time courses then highlighted in magenta and its onset time, time-to-peak, peak amplitude, and baseline diameter will be marked by red circles in the graphs below. Then right-click anywhere on panel two with a cross cursor to view and explore all traces for the selected subject ID or tree ID in panel three.Select a time course in the top graph of the left column by left-clicking on a trace. The selected trace will be highlighted in magenta in the graph and descriptive parameters of the database entry will be displayed on top of the graph. The corresponding onset time, time-to-peak, peak amplitude, and baseline diameter are displayed in the graphs below.The time course in thick black is the average of all displayed traces. Left-click on the export set button to save traces displayed in the top graph into the NNE 2.0 folder. Please make sure none of the exported files are open during the export action.If one of the files is open, a warning will appear. In this case, the user should close the exported file and restart NNE 2. To inspect all data for subject instead of tree, close panel three, restart NNE 2.0, then after repeating the selection of categories in panel one as before, select all data for subject in panel two.Right-click anywhere in panel three with a cross cursor to go to panel four to explore reference images and 3D image stacks for all traces in the top graph of panel three. Please know that panel four will open only if option all data for tree was selected in panel two. If all data for subject were selected instead, the user will be prompted to change the selection and direct it to panel one.Select a time course by left-clicking on it in the graph on top of the left column. At the bottom right of the left column, explore the corresponding reference image which in this case is loaded automatically from the hana_refs folder. At the bottom left of the left column, explore the corresponding 3D image stack loaded automatically from the hana_stk folder.Scroll through this stack using the arrows or slider below the figure. When the stack image reaches the level of the reference image, the stack image is highlighted and indicated as frame level. Click export set in the right column to export the highlighted time course into a file ref_stacks_trace.xls which is saved to the NNE 2 folder. Finally, close panel four to go back to panel one to start exploring a new set of data or close panel one to end the program. To use the functional measurements along with the 3D vascular structure, a corresponding image stack is located in folder hana_stk using its stack reference name displayed in panel four.To recognize the particular diving arterial, the user can refer to a low magnification map of surface vasculature with diving segments of measured arterial or trees labeled with corresponding numbers. This stack index number at frame level localizes the measurement within appropriate depth. The branching order along with the scan trajectory, localizes the measurement within the imaging plane.Taken together, the user is provided with 3D topography of vasculature populated by stimulus induced vasomotion at multiple locations within vascular trees. And NNE 2 was written to share the vascular imaging data of a specific study but with the intention of developing a simple tool for sharing and exploring data of similar kind by other users. In the prerequisite for using NNE 2 is a template, is a database in the format of a matrix And this could be achieved either by processing the data directly in MATLAB or using tools to build the matrix from other formats.In NNE 2 has the potential to help sharing experimental data across research communities. Facilitating further utilization of the data as well as the development for standards for data acquisition and processing.

Research

JoVE Journal

Neuroscience

Chronic Imaging of Mouse Visual Cortex Using a Thinned-skull Preparation

In vivo imaging using two-photon laser scanning microscopy (2PLSM) allows the study of living cells and neuronal processes in the intact brain. The ...

Transfection of Mouse Retinal Ganglion Cells by in vivo Electroporation

Transfection of Mouse Retinal Ganglion Cells by in vivo Electroporation

The targeting and refinement of RGC projections to the midbrain is a popular and powerful model system for studying how precise patterns of neural ...

Retrograde Fluorescent Labeling Allows for Targeted Extracellular Single-unit Recording from Identified Neurons In vivo

Retrograde Fluorescent Labeling Allows for Targeted Extracellular Single-unit Recording from Identified Neurons In vivo

The overall goal of this method is to record single-unit responses from an identified population of neurons. In vivo electrophysiological recordings from ...

Functional Neuroimaging Using Ultrasonic Blood-brain Barrier Disruption and Manganese-enhanced MRI

Although mice are the dominant model system for studying the genetic and molecular underpinnings of neuroscience, functional neuroimaging in mice remains ...

Visualization and Genetic Manipulation of Dendrites and Spines in the Mouse Cerebral Cortex and Hippocampus using In utero Electroporation

Visualization and Genetic Manipulation of Dendrites and Spines in the Mouse Cerebral Cortex and Hippocampus using In utero Electroporation

In utero electroporation (IUE) has become a powerful technique to study the development of different regions of the embryonic nervous system 1-5. To date ...

Fast Micro-iontophoresis of Glutamate and GABA: A Useful Tool to Investigate Synaptic Integration

One of the fundamental interests in neuroscience is to understand the integration of excitatory and inhibitory inputs along the very complex structure of ...

Live Imaging of Mitosis in the Developing Mouse Embryonic Cortex

Although of short duration, mitosis is a complex and dynamic multi-step process fundamental for development of organs including the brain. In the ...

Two-Photon in vivo Imaging of Dendritic Spines in the Mouse Cortex Using a Thinned-skull Preparation

Two-Photon in vivo Imaging of Dendritic Spines in the Mouse Cortex Using a Thinned-skull Preparation

In the mammalian cortex, neurons form extremely complicated networks and exchange information at synapses. Changes in synaptic strength, as well as ...

A Simple and Inexpensive Method for Determining Cold Sensitivity and Adaptation in Mice

Cold hypersensitivity is a serious clinical problem, affecting a broad subset of patients and causing significant decreases in quality of life.  The cold ...

A Simple One-step Dissection Protocol for Whole-mount Preparation of Adult Drosophila Brains

A Simple One-step Dissection Protocol for Whole-mount Preparation of Adult Drosophila Brains

There is an increasing interest in using Drosophila to model human brain degenerative diseases, map neuronal circuitries in adult brains, and study the ...