Below you will find the guidelines for submitting software. Download the guidelines as a PDF here.
Mission and Scope of Software Submissions
Aperture Neuro recognizes the essential importance of software to the advancement of science, especially in neuroimaging research. When submitting Software Research Objects to Aperture Neuro, authors are welcome and encouraged to think broadly beyond the traditional PDF of “Software” and “Toolbox” papers.
As for any Aperture Neuro Research Objects, software submissions will be selected and reviewed based on their quality, impact, relevance, and their ability to increase connectivity among researchers in the field. The software should fall within the interest of the OHBM mission to advance the understanding of the anatomical and functional organization of the human brain with a strong focus on neuroimaging. Research Objects involving animal studies are also welcome.
Submissions that report minor plug-ins for existing software or minor advancements of existing algorithms with limited breadth or impact are unlikely to be selected for peer review. However, submissions representing important changes (even if small) in a previous toolbox/library, but with great impact and utility, are very much welcome.
Almost every active researcher in the field of neuroimaging develops software in one way or another, and many research labs have their specialized in-house software. Aperture Neuro aims to publish code that is likely to have a broader utility (beyond one’s own lab). Due to the extensive workload for reviewers to assess code, not every submission may make it to peer review unless it is deemed to be of broader utility to the community.
Types of Software Submissions
Types of code submissions can be, but are not limited to the categories below:
Software and toolboxes: Authors can submit stand-alone software packages and toolboxes for neuroimaging analyses.
Examples: AFNI, TDT Decoding toolbox, PMC Toolbox, CVMANOVA toolbox, etc.
Notebooks and pipelines: Authors can submit Notebooks (E.g., Jupyter, R) and scripts (e.g. Python, Matlab/Octave markup code). While Aperture Neuro would prefer open source software (i.e., Python, Octave), Matlab is welcome too (as it can be widely distributed and can be compiled). The editorial team will consider submissions of non-open software on a case by case basis.
Notebooks can be educational in nature, they can contain pedagogical tutorials, they can reveal insights into specific analysis steps, and/or they can be entire processing pipelines. Submissions should include as much supporting information as possible. Documentation should be included within the notebook/mockup file.
Examples: BrainWavelet Matlab filters, Jupyter Notebook for simulating fMRI PSF, Python Pipeline HyPyP for hyperscanning, BV Notebooks, PrF fitting in Python, etc.
Apps and Web tools: Submissions can be smartphone apps for Android/iPhones and/or cloud-based or browser-based software. Such apps could, for example, serve an educational purpose regarding neuroimaging data acquisition, data reconstruction, brain science, or other topics.
Examples: Phone apps Kspapp, BrainTutor. Web-based analysis tools: MRI-Cloud, GiraffeTools, BioimageSuite, etc.
Brain imaging data acquisition and reconstruction code: Submissions can be open code related to MRI sequences, MR-signal simulation, and/or MRI image reconstruction (or other brain imaging modalities). Non-open sequence code that is confined to the programming environment of commercial vendors does not fall within the scope of Aperture Neuro’s code submissions.
Examples: ODIN, Pulseq, TOPPE, JEMRIS, Gadgetron programs, etc.
Requirements of Software Submissions
Authors are encouraged to submit software that is open-source and accessible via a trusted repository. Please link to this repository in the form on the Submission Platform. While any software that may have significant impact on the field may be submitted, Aperture encourages authors to submit software that fulfills the following criteria. Deviations from these criteria should be explained in the cover letter.
Preparing your Software submission
Authors will log onto the Aperture Neuro Journal Submission Dashboard to begin the submission process. When you are ready to submit your Research Object, please use your ORCID ID to log in. Once we receive your Research Object, you will be notified via email.
Cover Letter: Please include a cover letter with your submission. You will be asked to upload your cover letter as a separate document in the submission platform. This letter should be addressed to Aperture Neuro’s Editorial Team and include any relevant information you feel will aid the Editors in the consideration of your work.
Title: Titles are limited to 300 characters and should contain major keywords. Please do not use Subscript, Superscript, boldface and/or italics in your title.
Authors: The first author or first listed author should be the main contributor of any code or software submitted. Contributions from co-developers should be acknowledged.
Comprehensive Summary: All Software submissions must include a comprehensive summary that will serve as a “front page” of your submission. This summary should describe the main purpose of the software to Aperture Neuro’s readership and should place the software into context. This is different from the cover letter to the Editor. Keep the lay-public in mind as this summary will be the first thing audiences will see when visiting your publication on the Aperture Neuro site.
There is no particular requirement regarding the format or style of your summary (feel free to structure your summary as you see fit). Enter your comprehensive summary text in the Summary/Full Research Object step in the submission process.
For software submissions, we recommend that your summary should cover the following (if applicable):