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Thank you for your interest in the open data, tools, and other free resources produced by the Allen Institute.
To use our resources in your noncommercial research or for noncommercial purposes, you must cite them in accordance with this policy. Uses include analyzing our data, including our data in your manuscript or grant, using our analysis tools on your own data, using or annotating images in figures, including data or images in presentations, and more. This citation policy applies to data, tools, images, lab resources, code, protocols (including those hosted on protocols.io), and any other resources found on alleninstitute.org, brain-map.org, allencell.org, explore.allenimmunology.org, and all publications produced by Allen Institute teams, including preprints.
While not required, we appreciate it when researchers send us a copy of their publication or other work citing our open resources. This helps us track when and how our Content is being used, and thus guides and supports our continued efforts to provide useful open public resources. Please email us at [email protected] or contact us on social media.
If you cite or display any Content, or reference our organization, in any format, written or otherwise, including print or web publications, presentations, grant applications, websites, other online applications such as blogs, or other works, you must follow these Citation Guidelines. If you use specific images or other data, please cite the specific image or data used and the URL that links directly to that information in a manner that would allow a third party to navigate to that image or data on the Site, in addition to citing the resource that the image or other data is from as indicated below.
In cases where there is a primary publication about the specific resource, cite both the publication and the specific dataset. Citation of the primary publication, where one exists, is required when citing the data resource in a scientific publication. Follow the examples below to cite the dataset and applicable primary publications. Example citations are given in APA format. For a complete list of publications, see our lists of publications for Neuroscience at the Allen Institute, Allen Institute for Cell Science, and Allen Institute for Immunology. When integrating our data into a website, for example, using our application programming interface (API), cite the source in a manner that is clear, accurate and easily discoverable and link to the source dataset. Also, be sure that our content is never displayed in the absence of such citation. A citation must appear on the same page where the Allen Institute data or image appears.
Please see the Allen Brain Map Knowledge Base at knowledge.brain-map.org for the proper citation for each dataset, code, and other resource from the Allen Institute for Brain Science and MindScope Program.
Please see the Allen Cell Explorer at allencell.org/citation-policy for the proper citation for each dataset, code, and other resource from the Allen Institute for Cell Science.
You are encouraged to incorporate images from Allen Institute datasets into your publications. For example, you may wish to include a slide from the Allen Mouse Brain Atlas on its own, or in a larger figure that also includes your own data.
When citing anatomic reference atlas content without additional data, cite the anatomic reference atlas specifically. For example, when using the Allen Reference Atlas – Developing Mouse Brain, use only the reference atlas citation below and do not also cite the Allen Developing Mouse Brain Atlas as the source. When using the anatomical reference content in conjunction with data from an associated dataset, cite both the associated dataset and the reference atlas individually in your reference list.
To see the citation for each reference atlas from the Allen Institute for Brain Science and MindScope Program, please see the Allen Brain Map Knowledge Base at knowledge.brain-map.org. This example demonstrates how to cite images used in a figure; the same guidelines apply to figures that also incorporate data/images that are not from the Allen Institute.
Figure 1: Calbindin expression patterns and projection of calbindin-expressing neurons. A: Nissl (left) and anatomical annotations (right) from the Allen Mouse Brain Atlas and Allen Reference Atlas – Mouse Brain, at the same slice position as B and C. Allen Mouse Brain Atlas, mouse.brain-map.org and atlas.brain-map.org. B: Expression of Calb1 in adult mouse brain. Allen Mouse Brain Atlas, mouse.brain-map.org/experiment/show/71717640. C. Cre-dependent AAV tracing of axonal projections from an injection site in the primary motor area reveal projections of calbindin-expressing neurons. Projection targets include within the injection site (primary motor area), sites proximal to the injection (secondary motor area, primary and supplementary somatosensory area), and additional sites with somatomotor function (caudoputamen and posterior complex of the thalamus). Projections are primarily ipsilateral, with contralateral projections to mainly primary motor and somatosensory areas, as well as caudoputamen, via corpus callosum. Allen Mouse Brain Connectivity Atlas, connectivity.brain-map.org/projection/experiment/477836675. D. 3D representation of the projections in C with the 3D Brain Explorer.
In the references section, cite:
Allen Institute for Brain Science (2004). Allen Mouse Brain Atlas [dataset]. Available from mouse.brain-map.org.Allen Institute for Brain Science (2011).
Allen Reference Atlas – Mouse Brain [brain atlas]. Available from atlas.brain-map.org.
Daigle, T. L., et al. (2018). A Suite of Transgenic Driver and Reporter Mouse Lines with Enhanced Brain-Cell-Type Targeting and Functionality. Cell, 174(2), 465–480.e22. https://doi.org/10.1016/j.cell.2018.06.035
Lein, E.S. et al. (2007). Genome-wide atlas of gene expression in the adult mouse brain, Nature 445: 168-176. https://doi:10.1038/nature05453
Harris, J. A. et al. (2019). Hierarchical organization of cortical and thalamic connectivity. Nature 575, 195-202. https://doi:10.1038/s41586-019-1716-z
Oh, S.W. et al. (2014). A mesoscale connectome of the mouse brain, Nature 508: 207-214. https://doi:10.1038/nature13186
If you are using an image from the Allen Institute in a website, article, or other context that does not use academic citation formats, use the following citation:
For images from brain-map.org: Image credit: Allen Institute for Brain Science. [Link to specific URL of page where image is found.]
For images from allencell.org: Image credit: Allen Institute for Cell Science. [Link to specific URL of page where image is found.]
For images from alleninstitute.org: Image credit: Allen Institute. [Link to specific URL of page where image is found.]
For images from explore.allenimmunology.org: Image credit: Allen Institute. [Link to specific URL of page where image is found.]
White papers and protocols: When citing a white paper or other document associated with a particular resource, cite the specific document by title and date, as well as the Site for that atlas or resource. When using code or software tools, cite the code or software tool as shown in the Allen Brain Map Knowledge Base or Allen Cell Explorer Citation Policy. If you also used data from the Allen Institute for Brain Science or Allen Institute for Cell Science, cite both the code and the data separately.
For any code not specifically listed in the Allen Brain Map Knowledge Base or Allen Cell Explorer Citation Policy: Follow this formula for constructing a citation, using the year indicated in the code. Institute that developed code [Allen Institute for Brain Science, Allen Institute for Cell Science] (year). Name of code base [software package]. Available from [link].
Protocols: See information on each protocol for details. Generally, follow the format of: Allen Institute for Brain Science, Allen Institute for Cell Science, or named protocol author (year). Protocol name. Available from: link.