NeuroMorpho.Org is a web-based inventory dedicated to densely archive and organize all publicly shared digital reconstructions of neuronal morphology. Digital reconstructions archived in NMO come from two sources:
mining and mirroring of available online archives
direct peer-to-peer request from individual laboratories and investigators.
This data is collected and uploaded to the website by the NMO administrators.
Q:
Why is NeuroMorpho.Org needed?
A:
Digital reconstructions are a parsimonious and efficient representation of neuronal morphology. They allow extensive analysis and implementation of biophysical models of electrophysiology. However, reconstructing neurons is a very labor-intensive and time-consuming process. A collection of such data is an invaluable resource for the neuroscience community. This inventory is meant to encourage data sharing among neuroscientists, enabling further use of this data and to prevent data loss.
Q:
Who started and maintains NeuroMorpho.Org?
A:
NeuroMorpho.Org was started and is maintained by the Computational Neuroanatomy Group at the Krasnow Institute for Advanced Study, George Mason University, under the direction of Prof. Giorgio Ascoli, PhD. This project is part of a consortium for the creation of a "Neuroscience Information Framework," endorsed by the Society for Neuroscience, funded by the National Institutes of Health, led by Cornell University (Dr. Daniel Gardner), and including numerous academic institutions such as Yale University (Dr. Gordon Shepherd), Stanford University (Dr. Paul Sternberg), and University of California, San Diego (Dr. Maryann Martone).
Q:
What kind of digital reconstructions does NeuroMorpho.Org accept?
A:
NeuroMorpho.Org accepts digital reconstructions from any and all animal species, brain regions, developmental stages, experimental preparations, and imaging techniques. Moreover, neuronal reconstructions of incompletely stained cells, without reliable diameter information, or only traced in two dimensions or with some disconnected branches, are also useful and can be deposited with appropriate disclaimer notes.
However not all digital representations of neuronal morphology are suitable for inclusion in the database. NeuroMorpho.Org only archives branching structures (axons and/or dendrites) traced into sequences of interconnected points or vectors (typically visualized as cylinders or truncated cones) as in the popular Neurolucida, Bitplane, NeuronJ, Amira, and Eutectic systems. Surface contours (typically traced from electron-microscopy), voxel-based image stacks (often created from confocal microscopy), and pencil-on-paper tracings (using camera lucida) fall outside the scope of this database unless they are also converted to vector format.
Q:
What is the "NeuroMorpho.Org ID"?
A:
Each reconstruction in NeuroMorpho.Org is now identified by a unique number,
for example NMO_00001.
The NeuroMorpho.Org ID can be used to reference specific reconstructions downloaded from the website and used in your publication(s)
(in addition to other requirements outlined in the Terms of Use).
Q:
What kind of information is associated with each neuronal reconstruction?
A:
NeuroMorpho.Org associates 3 types of information with each neuronal reconstruction:
General information (Metadata) of the reconstruction extracted from corresponding publications.
Name of researcher and laboratory providing the reconstructions
Publications associated with each reconstruction
Web URL of archives (if available) with any additional information about the reconstruction
Subject-related information - species, strain, age, weight, gender
Experiment-related information - protocol, experimental condition, staining method, slicing direction and thickness, objective type and magnification.
Brain region at three levels: main region/structure, sub-region, detailed sub-region (example: Hippocampus, dentate gyrus, granule cell layer)
Neuron type at three levels: main neuron class type, sub-class, detailed sub-class (example: Interneuron, basket cell, nested)
Reconstruction method
Format of original data
Original and standardized versions of the data file, along with a log of changes before and after the Standardization process.
A set of 21 pre-computed morphometric measurements
Q:
How can NeuroMorpho.Org help my project?
A:
Digital reconstruction of neuronal morphology can be used for comparative morphological and stereological analysis, compartmental simulations of neuronal electrophysiology, computational models of structure and development, scientific education, and anatomically realistic neural networks. For more information, please refer to this short review, or browse the Tools & Links page.
Please refer to the Terms of Use, including the disclaimer, citation requirements, and note to developers.
Q:
Does NeuroMorpho.Org use cookies?
A:
NeuroMorpho.Org uses session cookies. Session cookies enable you to better navigate the website and download neuron related data. Without cookies, you can still browse the website but you will not be able to download the neuron related files.
Q:
How are the number of Downloads counted?
A:
The number of downloads displayed on the Homepage represents the number of neuron files + auxiliary files downloaded from the website.
The number of downloads displayed in the Detailed Statistics page represents only the number of neuron files downloaded.
Q:
How are the number of Hits counted?
A:
A distinct IP address that visits the website is counted as an individual hit. The hits counter is not incremented if the currently visting IP address is the same as the previous one. Non-consecutive access to the website adds to the counter.
Q:
What is the relationship between NeuroMorpho.Org and other reconstruction repositories (e.g. Duke-Southampton archive)?
A:
While some existing repositories allow upload from external investigators, most available collections contain data from single-labs. NeuroMorpho.Org, on the other hand, is a curated inventory; a centralized resource pooling data from multiple sources.
Q:
Where can I find original microscopic images of neurons?
A:
The Cell-Centered Database is an imaging resource. You can also contact the individual data owners of reconstructions you find in NeuroMorpho.Org.
Q:
Can I receive an email notification when new reconstructions are added to the database?
A:
Yes, please register for the free email-based support group by sending your e-mail address through Contact Us.
Q:
I have digital reconstructions of neuronal morphology, which I am willing to share. What should I do?
How do I obtain the number of hits matching my search criteria before running a search?
A:
In both the Search by Metadata and Search by Morphometry pages, the "Hits from current criteria" button returns the number of hits matching the selected criteria. This may be useful to fine tune the search, narrowing down or expanding the results to the desired number before retrieval.
Q:
Is there overlap between categories in Development? (Metadata>Animal>Development>Young, Adult, Old, Not reported)
A:
This categorization is species-specific and based on what has been reported in the publications. Usually, a specific age-range which is often also reported in the publications, is included in the Details page of each reconstruction.
Q:
How are "Cell Types" determined?
A:
The topics of neuronal classification, and even neuronal nomenclature, are far from settled in the scientific community. While we await (and contribute to) consensus among researchers on these topics, we are simply adopting the descriptive terminology reported in the published paper associated with the reconstructions.
Q:
What does "Not reported" mean?
A:
When certain information in the categories of Metadata are not included in the publications this is marked as "Not reported"
Q:
Why do some links to PubMed cause a browser problem in Linux?
A:
Due to recent changes in the PubMed website there may be certain incompatibilities between Firefox browsers and Pubmed links. This may cause a problem when you click on the Pubmed Link button in the neuron details page. You can find a list of browsers that work well with PubMed's recent changes in PubMed FAQs.
Q:
How can I use "Search by Keywords"?
A:
"Search by Keywords" allows the user to input free text as a search criteria. You can type in several keywords at a time, but they must be separated by a comma (,).
Q:
What are acceptable terms for "Search by Keywords"?
A:
For this version, acceptable terms are those that you can see in drop-down menus in the Metadata page. You can type in any combinations of these terms. Our search engine will compute the most logical way of interpreting these terms. Search terms will be linked with the Boolean operator OR if they refer to the same domain (e.g. "hippocampus, cerebellum", or "cat, rat"), and the Boolean operator AND if they refer to different domains (e.g. "basket cell, biocytin").
Terms are not case sensitive, but plurals are not allowed in this version. Any term(s) not considered acceptable will be pointed out and the user will have an option to modify the search or continue without the term(s).
Q:
What do the sample values in "Search by Morphometry" represent?
A:
The total available data for a given Search Criteria based on the selected Search Specificity is divided into the following statistical sample values: minimum value, 1st quartile, median, 3rd quartile, maximum value.
Q:
Can NeuroMorpho.Org be accessed directly by external queries?
A:
Yes, data can be retrieved from NeuroMorpho.Org automatically through external queries. This feature enables powerful searches through resources designed to mine and integrate neuroscience data. If you are interested in this function please Contact Us.
Q:
What is the "Neuron Atlas"?
A:
Based on and adapted from the Brain Explorer application of the Allen Brain Institute, Neuron Atlas is a visualizer of rodent neurons available in NeuroMorpho.Org. Neuron Atlas enables 3D browsing with interactive features that are similar to the Neuron Viewer available in the Details page of each neuron in NeuroMorpho.Org. For more details and to download the application, see Neuron Atlas
Q:
What does "Literature coverage" mean and why is it included?
A:
"Literature coverage" provides the detailed results of the extensive search undertaken by NMO to populate this database. The user can search for inclusion of a publication in our database through a PMID search. The user can also browse publications that were positively identified as containing digital reconstructions and check the data availability status for each publication.
Q:
What is a PMID?
A:
A PMID is a PubMed Identifier. It is a unique number assigned to each PubMed citation of life sciences and biomedical scientific journal articles.
Q:
What is "Random neurons"?
A:
"Random neurons" displays a random selection of neurons in the database. This option provides one-click access to representative samples of reconstructions.
Q:
What is the Search functionality in the Detailed Statistics page?
A:
To quickly retrieve the site unique visits from specific countries and the download activity of specific cell types, brain regions, species, and archives, enter the desired keyword (e.g. "Italy" or "Hippocampus") in the respective Search boxes. This will return the corresponding values for the specified entry.
What is a digital reconstruction of neuronal morphology?
A:
Experimental and theoretical studies demonstrated that dendritic and axonal structures are crucial determinants of neuronal activity, plasticity, and connectivity in both normal and pathological states. The stunning heterogeneity of neuronal shape is possibly an essential feature of the functional complexity of the nervous system.
In the course of various anatomical, electrophysiological, and pharmacological research projects, neuronal arborizations are visualized under a microscope. The three-dimensional digital reconstruction of these images is an important step in the quantitative investigation of cellular neuroanatomy. In this process, neurites are semi-manually traced through the use of specialized computer software and represented as binary trees of branching cylinders (or truncated cones). The process has several steps:
preparing biological samples
preparing slides from the samples
staining the slides
imaging the slides
tracing the neuronal arborizations
editing and saving the reconstruction file
Q:
Are the original reconstructions processed before inclusion in NeuroMorpho.Org?
The three dimensional structure of a neuron can be represented in a SWC format (Cannon et al., 1998). SWC is a simple Standardized format. Each line has 7 fields encoding data for a single neuronal compartment:
Every compartment has only one parent and the parent compartment for the first point in each file is always -1 (if the file does not include the soma information then the originating point of the tree will be connected to a parent of -1). The index for parent compartments are always less than child compartments. Loops and unconnected branches are excluded. All trees should originate from the soma and have parent type 1 if the file includes soma information. Soma can be a single point or more than one point. When the soma is encoded as one line in the SWC, it is interpreted as a "sphere". When it is encoded by more than 1 line, it could be a set of tapering cylinders (as in some pyramidal cells) or even a 2D projected contour ("circumference").
Q:
What are the pre-computed morphometrics?
A:
Several morphological measurements have been extracted from each neuronal reconstruction and stored inNeuroMorpho.Org. These parameters can be used to "Search by Morphometry", and their values are reported in the detail pages for the individual cells.
Soma surface area
Total number of trees
Total number of bifurcations
Total number of branches (bifurcations plus terminations)
Neuronal height (95% of first principal component)
Neuronal width (95% of second principal component)
Neuronal depth (95% of third principal component)
Average branch diameter
Total arborization length
Total arborization surface area
Total internal volume of the arborization
Maximum Euclidean (straight) distance from soma to tips
Maximum Path (along the tree) distance from soma to tips
Maximum Branch order (number of bifurcations from soma to tips)
Average Contraction (the ratio between Euclidean and path length calculated on each branch)
Total number of reconstruction points
Topological asymmetry (average over all bifurcations of the absolute value of (n1-n2)/(n1+n2-2), where n1 and n2 are the numbers of tips in the two subtrees)
Rall's Ratio (average over all bifurcations of the sum of the diameters of the two daughters, elevated to 1.5, divided by the diameter of the parent, elevated to 1.5)
Local Bifurcation angle (average over all bifurcations of the angle between the first two daughter compartments)
Remote Bifurcation angle (average over all bifurcations of the angle between the following bifurcations or tips)
For exact definitions and/or more information about these measurements, please visit the L-Measure website. Note that each of these parameters is extracted from the whole neuron (axon plus dendrites). L-Measure allows the user to specify any sub-portion of the neuron to compute measurements and also contains a much larger number of morphometrics.
Q:
How are different parts of the neurons color coded in visualization?
A:
NMO uses the Cvapp application for visualizing neurons. Cvapp associates a color to each compartment type. In the SWC format there is a non-enforced rule for types:
Compartment
Associated type
Associated color
soma
1
white
axon
2
gray
basal dendrite
3
green
apical dendrite
4
magenta
Q:
How is Tissue shrinkage reported?
A:
Publications report tissue shrinkage in various formats. If available, these values are standardized and reported in NeuroMorpho.Org as percentages.
Q:
How is the soma format represented in the standardized (CNG.swc) files?
Why are certain reconstructions assigned to more than one Archive?
A:
Reconstructions resulting from collaborations between multiple laboratories can be assigned to more than one Archive.
Q:
What is AutoNeuron?
A:
AutoNeuron is an extension module of Neurolucida (MBF Biosciences, Inc), the tracing and reconstruction software system. AutoNeuron’s tracing algorithm scans 3D image stacks and automatically traces the neuron and identifies soma and neurites.
If your question is not listed here, please Contact Us.
0
