Automated Manuscript Precheck

Before you submit to [JATIS], you are encouraged to upload your manuscript to the Penelope.ai precheck tool, which is free to SPIE journal authors. This tool performs an automated assessment of your manuscript for the journal’s formatting requirements, and reduces the number of times papers are sent back to authors for formatting fixes.

This tool only works with filetypes ending in .docx. If your paper was authored in LaTex or another writing program, consider exporting it as a Word document to use this tool. You can then submit your manuscript to the journal in any of the accepted file types (.doc, .docx, .pdf, or .tex).

You will be asked to upload a .docx file and provide your name and email address. The results will be sent to your email address within a few minutes.

Publication Policies

The following requirements will permit you to determine if you can submit a paper to an SPIE journal.

Rights and Permissions: Prior to submission, authors should obtain all clearances, authorizations, and licenses needed for submission and publication. Upon acceptance, authors are required to complete a Creative Commons CC BY license authorizing SPIE to publish the paper.

Significance: Contributions should be substantial and significant in content. We may decline to publish papers that report only incremental progress. Although a paper may be correct and appropriate for an SPIE journal, if it does not demonstrate, in the estimation of the reviewers and editor, sufficient new and important information to warrant publication, or provide a comprehensive review of the current state of the art, it will be declined. Manuscripts that are commercial in nature will not be considered.

Originality: Papers should describe the original work of the authors that has not been previously published in a refereed journal and is not currently under consideration for publication in another refereed journal. SPIE does not allow or sanction duplicate or concurrent submissions of a paper to more than one peer-reviewed journal. Any copying of text, figures, data, or results of other authors without giving credit is defined as plagiarism and is a breach of professional ethics. Such papers will be rejected and other penalties may be assessed. 

Double Publication: Papers should not report work that the author has already published in another refereed journal. This is also an ethical violation. Such papers will be rejected and other penalties may be assessed.

Previously Rejected Papers: If you are submitting a new version of a paper that was previously submitted to an SPIE journal and was declined, there is an entry on the submission form to indicate this. Follow the instructions there, and in a cover letter, indicate the paper number and title, and briefly describe the changes that have been made to warrant a new submission. Copies of rejected manuscripts are retained in the journal's editorial system.

Note: SPIE journal policy is that after a reject decision, resubmission of a manuscript will normally only be accepted after three months have elapsed since the decision date. This policy is intended to ensure that adequate time is available between the reject decision and resubmission to address the major changes and rewrite that are normally required to address the concerns leading to a reject decision.

Rejection by Another Journal: If the paper has been submitted to another journal and rejected, and if you believe that submission to one of SPIE's journals would be more appropriate, you are urged to take into account any comments or suggestion for improvement from your previous submission. Our reviewers will usually find the faults identified by previous reviewers.

Conference Proceedings Papers

Submissions to SPIE journals based on reports that have been submitted to or published in a conference proceedings should adhere to the following guidelines:

Distinction between proceedings and journal papers: Conference proceedings provide a vehicle for rapid reporting of ideas, techniques, and results. It is not uncommon for these reports to be somewhat incomplete and inconclusive. The purposes of proceedings papers range from snapshots of recent or continuing work to the reporting of a completed work or project. Journal papers are expected to be original, complete, and polished; to contain comparisons of theoretical and experimental results; and to include substantial conclusions and comprehensive references to other work.

Revision of conference proceedings manuscripts for journal submission: SPIE publication policy permits manuscripts based partly or entirely on scientific content previously reported in SPIE proceedings to be submitted to SPIE journals. Furthermore, SPIE permits manuscripts based partly or entirely on scientific content previously reported in a non-SPIE conference to be submitted to SPIE journals so long as the copyright policies of the non-SPIE conference are properly adhered to (see below). In most cases, it is anticipated that the journal submission will represent a substantively expanded, refined, or otherwise revised manuscript relative to the proceedings paper to fully satisfy the standards of significance, originality, and presentation quality expected in a journal submission that is being considered for acceptance through the journal peer-review process. A manuscript submitted to an SPIE journal that incorporates minimal or no revisions over a prior or concurrent SPIE proceedings paper may be considered for publication in an SPIE journal and admitted into the peer-review process provided the submission fulfills the requirements of significance, originality, and completeness expected in a journal submission. SPIE does not consider publication of an accepted journal article based on a prior proceedings paper to constitute double publication.

Disclosure: If a manuscript (or portion of a manuscript) was previously published in a conference proceedings or is under consideration for publication in a conference proceedings, this information must be disclosed when the manuscript is initially submitted to an SPIE journal. Authors should also reference or acknowledge the prior proceedings paper within the submitted journal article.

Copyright: SPIE copyright policy permits authors to submit derivations of their proceedings papers to their journal of choice. Submissions to SPIE journals are permissible provided the other expectations described herein are satisfied. Authors submitting to journals published by other publishers should verify that publisher's copyright and submission policies. Authors wishing to submit papers that were presented at or published in a conference proceedings sponsored by organizations other than SPIE are responsible for adhering to the copyright policies related to that presentation or publication and are expected to disclose the prior presentation or publication history of the submission.

Journal submission format: All proceedings manuscripts submitted to an SPIE journal must be prepared according to the guidelines provided here.

Integration with BioRxiv

Authors may submit a manuscript directly from the bioRxiv platform to Neurophotonics. To do so, follow these steps:

1. Go to the "Author Area" of bioRxiv
2. Select "Submit bioRxiv Preprint to a Journal"
3. Select Neurophotonics from the drop-down list.

The system will import the files and notify the corresponding author via email, with a link to complete the submission process. 

SPIE Guidelines for Ethical Publishing

Authors are expected to read and abide by the SPIE Guidelines for Ethical Publishing.

SPIE is a member of the Committee on Publication Ethics (COPE). 

Authorship

Authorship should be limited to those who have made a significant contribution to the concept, design, execution or interpretation of the research study. All those who have made significant contributions should be offered the opportunity to be listed as authors. Other individuals who have contributed to the study should be acknowledged, but not identified as authors. The sources of financial support for the project should be disclosed.

All collaborators share some degree of responsibility for any paper they coauthor. Some coauthors have responsibility for the entire paper as an accurate, verifiable, report of the research. These include, for example, coauthors who are accountable for the integrity of the critical data reported in the paper, carry out the analysis, write the manuscript, present major findings at conferences, or provide scientific leadership for junior colleagues.

Coauthors who make specific, limited, contributions to a paper are responsible for them, but may have only limited responsibility for other results. While not all coauthors may be familiar with all aspects of the research presented in their paper, all collaborations should have in place an appropriate process for reviewing and ensuring the accuracy and validity of the reported results, and all coauthors should be aware of this process.

Every coauthor should have the opportunity to review the manuscript before its submission. All coauthors have an obligation to provide prompt retractions or correction of errors in published works. Any individual unwilling or unable to accept appropriate responsibility for a paper should not be a coauthor.

Because authorship attribution requires accountability for the submitted work, SPIE does not allow ChatGPT and other Large Language Models (LLMs) to be listed as an author on a manuscript. If authors use AI tools when writing a manuscript, it must be disclosed along with all other tools used in the study in the Materials and Methods section of the paper. This section should describe which AI tool was used and how it was used. SPIE follows the guidance of COPE on this topic, which further advises that “Authors are fully responsible for the content of their manuscript, even those parts produced by an AI tool, and are thus liable for any breach of publication ethics.”

Collaborations are expected to have a process to archive and verify the research record; to facilitate internal communication and allow all authors to be fully aware of the entire work; and respond to questions concerning the joint work and enable other responsible scientists to share the data. All members of a collaboration should be familiar with, and understand, the process.

For guidance on preventing and resolving authorship problems, see “How to handle authorship disputes: a guide for new researchers” (a resource from the Committee on Publication Ethics).

Plagiarism Screening

SPIE defines plagiarism as the reuse of someone else's prior ideas, processes, results, or words without explicit attribution of the original author and source. Unauthorized use of another researcher’s unpublished data or findings without permission is considered to be a form of plagiarism even if the source is attributed. SPIE considers plagiarism in any form, at any level, to be unacceptable and a serious breach of professional conduct.

SPIE uses the Crossref Similarity Check plagiarism screening service to detect instances of overlapping and similar text in submitted manuscripts. Crossref Similarity Check is a multipublisher initiative to screen published and submitted content for originality.

Conflict of Interest

Real and potential conflict of interest should be avoided and disclosed to all impacted parties when it cannot be avoided.

There are many professional activities of scientists and engineers that have the potential for a conflict of interest. Any professional relationship or action that may result in a conflict of interest must be fully disclosed. When objectivity and effectiveness cannot be maintained, the activity should be avoided or discontinued.

Authors should clearly identify in the manuscript all financial and material support for their research and work under a Disclosures header before the Acknowledgments. If the authors have no relevant financial interests in the manuscript and no other potential conflicts of interest to disclose, a statement to this effect should also be included in the manuscript.

A helpful form with guidelines for generating a disclosure statement is available from the International Committee of Medical Journal Editors website (see http://www.icmje.org/conflicts-of-interest/). This form should not be uploaded with a manuscript submission; it is only a tool to help authors generate a disclosure statement.

Use of Human Subjects and Animals

SPIE expects all authors to observe internationally accepted principles and practices related to the ethical conduct of research involving the use of human subjects or animals. A brief statement must be included in the manuscript identifying the institutional oversight or licensing body that approved the studies. For studies involving human subjects, a statement must also be included confirming that informed consent was either obtained from all subjects or this requirement was waived by the oversight body.

Authors must obtain written permission from the subject (or parent/guardian, if the subject is a minor child) to publish a photograph with an identifiable human face. Such photographs should be used only when scientifically relevant.

Overview

Manuscripts should be submitted in English, and the presentation should be as succinct as comprehension will permit. Manuscripts are reviewed and refereed. Those accepted for publication are edited for conformance to the journal's style.

How to Write a Good Scientific Paper by Chris Mack is a useful guide on writing for a peer-reviewed journal. Click here to download the full PDF of this free SPIE ebook.

For peer review, manuscripts should be submitted with the figures/tables and their captions incorporated into the same file as the manuscript text. However, upon first revision or acceptance, authors will be asked to submit individual figure files and a properly formatted manuscript for use in production. The total combined limit for submission files is ~100 MB. 

SPIE journals typically allow only one round of major revision. Authors should carefully address all reviewer comments when submitting a revised manuscript. 

Claims of "new" or "novel" work or of being the "first" to report on a topic should be avoided unless they can be fully substantiated.

Cover Letter

Authors are required to include a separate cover letter with their submission explaining the significance and novelty of the work, the problem that is being addressed, and why the manuscript belongs in this journal. This cover letter sample (.docx) can be used as a template.

Authors submitting to a Special Section should include the title of the Special Section in their cover letter.

English Language Editing

For authors who want help improving language and grammar, AI tools, such as Grammarly or PaperPal, offer a low-cost editing option. In accordance with the rules stated in the Large Language Models section of these guidelines, such use of AI tools is acceptable but should be disclosed in the Acknowledgments section of the manuscript. 

Alternatively, authors may prefer a human professional edit. For this service, SPIE recommends Editage, which offers a 15% discount to SPIE authors. Please note that use of this service does not guarantee editorial acceptance by an SPIE journal. You should avoid making additional changes to your manuscript after receiving the edited version, as grammatical errors may be introduced. More detailed information can be found at editage.com/spie.

Large Language Models

Use of Large Language Models (LLMs) and other AI tools must be disclosed along with all other tools used in the study. The disclosure should describe which AI tool was used and how it was used. AI tools must be disclosed even for general uses, such as cleaning up language and grammar. AI tools used in such methodologies as data collection and figure creation should be disclosed in the Materials and Methods section of the paper. Use for language and grammar clean-up should be disclosed in the Acknowledgments.

Manuscript Types

Original research (requires a structured abstract - see "Parts of a Manuscript," below)

Research Paper: A full-length manuscript presenting original research. Neurophotonics does not limit the length of research papers. However, authors are strongly encouraged to stay focused and use concise, scientific language. It is expected that in most cases papers will not exceed 10,000 words, and there will be no more than 8 figures and/or tables. Additional figures and tables can be included in Supplemental Content.

Letter: A short technical communication of significant novelty and interest intended for rapid publication. The manuscript length for Letters may not exceed eight typeset journal pages. This corresponds to approximately 4000 words (excluding title, abstract, and author information); figures will further reduce the maximum word content (estimate 250 words per figure). Additional figures and tables can be included in Supplemental Content.

Technical Note: A concise description of a software package, instrument, chemical/biosensor, or procedure that provides a solution to a specific problem and has sufficient novelty and value to the Neurophotonics reader community. Additional figures and tables can be included in Supplemental Content.

Synthesis and Opinion

Review Paper: An article that provides exciting and insightful coverage of a particular topic or field. Reviews are typically invited/commissioned and written by highly regarded, leading experts in the field. Reviews summarize progress made in a particular development and/or application area of neurophotonics during a specified period, synthesize this progress with other advancements in photonics and/or neuroscience, summarize the current state of the art, and provide a visionary outlook for the next 5-15 years. It is expected that in most cases Reviews will not exceed 10,000 words, and there will be no more than 8 figures and/or tables.

Primer: A conceptual overview of a current or emerging neurotechnique including the basic technical background, its current applications, and outlook on the future impact. Reviews are typically invited/commissioned and written in language that can be understood by a broad Neurophotonics readership. Primers introduce in simple terms the basic technical background of the method, explain the advantages and the limitations of the technology, and highlight example neuroscience applications. It is expected that in most cases Primers will not exceed 10,000 words, and there will be no more than 8 figures and/or tables.

Perspective: A substantive article that provides forward-thinking assessment of a particular topic within neurophotonics where new, emerging ideas are balanced with scientific premise, feasibility, and the current state-of-the-art. Perspectives are expected to identify the current challenges and/or controversies. The goal of perspectives is to inform our broad readership and spark dialog that will help push the field forward. Perspectives are typically limited to less than 4,000 words; figures will further reduce the maximum word content (estimate 250 words per figure). Potential authors are encouraged to contact a member of the Editorial Board before writing the manuscript.

Opinion: A substantive article that provides a critical assessment of a specific approach or finding in the context of the current state-of-the-art. Like Perspectives, Opinions are expected to identify and discuss the challenges and/or controversies sparking dialog that will help push the field forward. Opinions are thought provoking, focused articles typically 1,500 to 3,000 words in length; figures will further reduce the maximum word content (estimate 250 words per figure). Potential authors are encouraged to contact a member of the Editorial Board before writing the manuscript.

Outlook: A focused visionary article that takes a speculative look at where a technology or a research area might be heading. Of particular interest are the prospects in the next 5-15 years. Outlook papers should include a brief overview followed by predictions for the future. Outlooks are typically 1,500 to 3,000 words in length; figures will further reduce the maximum word content (estimate 250 words per figure). Potential authors are encouraged to contact a member of the Editorial Board before writing the manuscript.

Step-by-step

Protocol: A step-by-step description of an original method (or its latest version) that the authors used to generate results published in a peer-reviewed journal. Protocols should contain a full list of parts and blueprints (e.g., for building optical instruments), reagents (e.g., for synthesis of optical probes), etc., and step-by-step instructions for assembly/synthesis/performing an experiment. Protocols should also contain highlighted critical steps, debugging/troubleshooting procedures, and guidelines for quality control and data analysis. We also encourage authors to submit videos for steps that are technically challenging. Neurophotonics does not limit the length of Protocols. However, it is expected that in most cases Protocols will not exceed 10,000 words, and there will be no more than 8 figures and/or tables. Additional figures and tables can be included in Supplemental Content.

Tutorial: An educational, introductory, and systematic description of a technology, method, or experiment. Tutorials discuss the rationale for developing or applying specific neurophotonic tools. The purpose of Tutorials is to introduce the tool in the context of the existing landscape and to provide comprehensive guidelines for the users in a way that enables the users to meaningfully tailor, optimize, and apply the tool for their own needs. Tutorials should be written in a language that can be understood by a broad Neurophotonics readership. Neurophotonics does not limit the length of Tutorials. However, it is expected that in most cases Tutorials will not exceed 10,000 words, and there will be no more than 8 figures and/or tables. Additional figures and tables can be included in Supplemental Content.

Informatics

Data Paper: A paper providing a detailed description of a research dataset. In most case, the dataset would be accompanied by description of methods used to acquire the data as well as data analysis tools. The goal is to facilitate sharing of raw and/or preprocessed data for secondary or meta-analysis. The dataset must be deposited in a public repository and must be made publicly available upon publication of the Data Paper. The manuscript length for Data papers may not exceed eight typeset journal pages. This corresponds to approximately 4000 words (excluding title, abstract, and author information); figures will further reduce the maximum word content (estimate 250 words per figure). Additional figures and tables can be included in Supplemental Content.

Features

News and Comment: A description of news and opinions on a topic of general interest to the readers of Neurophotonics.

Interviews: One-on-one conversations with highly regarded, leading experts in the field of neurophotonics, published in a video format.

Parts of a Manuscript

Title

The title of your paper should be descriptive and concise.

• Acronyms should be spelled out.
• Titles should not begin with the articles A, An, or The.
• Avoid use of the words "new" or "novel" in the title.

Authors and Affiliations

Provide full author names, including given name and family name. These names will be used in official databases and indexes. Initials are not allowed for the given name. Provide full affiliations, including institution, department, street address, city, postal code, and country. An email address should be provided for the corresponding author, and this person should be noted with a footnote.

Structured Abstract

Authors are required to use structured abstracts in their manuscript submissions of original research. The abstract should be a summary of the paper and not an introduction (200 words maximum). It should be self-contained (i.e., no numerical references) and substantive in nature, presenting concisely the following five categories:

• Significance: Provide the rationale or motivation for the work (i.e., its broad impact).
• Aim: Briefly describe the study, tools, or systems used.
• Approach: Briefly describe the materials and methods used.
• Results: Provide a core summary of study numbers, analyses, discoveries, or data descriptions.
• Conclusions: An interpretive statement that summarizes the approach and results of the work.

Subject terms or keywords

Keywords are required. Please provide 3-6 keywords related to your paper.

Parts of a research paper

Introduction: Provide a clear context for the study, present the problem or research question, review relevant literature, and outline the paper’s objectives and hypotheses.

Materials and Methods: Include a detailed explanation of the experimental procedures, the equipment and materials used, and the methodology employed, enabling replication of the study. Examples of materials may include cell lines, devices unique to the lab, or any purchased materials critical to the results reported in the paper.

Results: Present the findings of the study in a clear and concise manner, using tables, graphs, or text to depict the data collected, without interpreting or evaluating the results.

Discussion: Interpret the results in light of the research question, compare them with existing literature, explain the implications of the findings, and suggest areas for future research.

Text

Type manuscript single-spaced in a single column, using a readable font size (for example, 12-point type). Page numbers and line numbers must be included.

Note the following style points:

• Journal style does not permit the use of bold or italic fonts for emphasis of words in the text; these fonts should be reserved for math. 
• Words should be spelled using American English. 
• Spell out all abbreviations and acronyms at first use. 
• Metric units should be used unless to do so is not feasible or would result in a serious loss of clarity. 
• Footnotes are not allowed.

Equations

Create equations using MathType or Equation Editor 3.0. If using Word 2007 or later, the native equation editor can be used, but the document must be saved as .docx. When equations built with Microsoft's Editor are back-saved to the .doc format, they are converted to low-resolution graphics and will not be usable for composition. To use MathType or the old Equation Editor 3.0, you will need to select Object on the Text section of the Insert tab and then select MathType/Equation Editor in the drop-down menu. Variables should be written in italic font.

Biographies

Biographies of authors are published with each paper. Manuscripts should include a brief professional biography not to exceed 75 words. Authors are also encouraged to update their online SPIE profile with their photograph and biography on our website at http://spie.org/profiles/home. This profile will be linked to the published paper. 

Appendices

Any figures, tables, or equations in Appendices should continue the numbering sequence established in the body of the paper. Appendices may not be composed of only tables and figures; they must also include explanatory text and captions.

Disclosures

Conflicts of interest should be declared under a "Disclosures" header. If the authors have no competing interests to declare, then a statement should be included declaring no conflicts of interest. For assistance generating a disclosure statement, see the form available from  the International Committee of Medical Journal Editors website: http://www.icmje.org/conflicts-of-interest/.

Code and Data

In support of open scientific exchange, SPIE journals require Data and Code Availability statements in all accepted papers under the heading “Code and Data Availability,” which should follow the Disclosures section. These statements should provide access information regarding the computer code and data that would be required to replicate or interpret the findings reported in the paper. See the section below about Code and Data for more information about what to include in this section.

Acknowledgments/Funding Sources

Use this section to identify people who have aided the authors in accomplishing the work presented and to acknowledge sources of funding. Include grant numbers and the full name of the funding body. Funding information will be deposited to FundRef.

References

The purpose of a reference is to make the source easy for the reader to locate. To this end, each reference should provide as much information as is available. The basic elements of a reference include author names (including first initials), article/chapter title, journal or book title, volume number, issue number, page range, and year of publication. References are professionally copyedited on accepted manuscripts to conform to journal style, and authors do not need to spend a lot of time adapting references to the journal's reference format, so long as all of the required information is present.

References to published literature should be listed at the end of the manuscript and numbered consecutively in the order of their citation in the text. In-text citations can use superscript or bracketed reference numbers. Private communications or unpublished reports should be treated as references. Click here for sample book, journal, and internet references. For references with three or fewer authors, list all authors. For references with four or more authors, list the first author only followed by "et al."

Manuscript Templates

To make your initial submission process as easy as possible, and to make it easier for the editors and referees to review your manuscript, we require only a single PDF document containing the text and figures, along with any supporting multimedia files. The figures and their captions should be placed within the document, near the first mention of each figure in the text, and line numbers and page numbers should be included. For revised manuscripts, individual figure files and source files will be required.

Microsoft Word: A Microsoft Word template (.docx) is available to assist you with formatting. Use MathType for equations. Or, if using MS Word 2007 or later, the native equation editor can be used, but the document must be saved as .docx. Backsaving to .doc format will convert all equations to low-resolution graphics, which cannot be used for typesetting. Please note that all accepted papers are professionally typeset; the template is intended only as a guideline for author convenience, and it is not necessary to rigidly adhere to the format.

LaTeX: A LaTeX template (.zip) is available to assist you with formatting, or you can use the Overleaf authoring tool explained below. LaTeX manuscripts can be uploaded as a .zip file including the manuscript, locally compiled PDF, bibliography, and all referenced style files and figures; or, the files can be uploaded separately. Please include all style files that are referenced in the .tex manuscript (such as .cls, .bst, .sty, etc.). Upon submission, choose file type "Merged PDF" for the locally compiled PDF; select "Bibliography" for .bib files; and select "LaTeX Supplementary File" for .cls, .bst, . sty, and any other associated style files. Do not include the README.txt file in the upload. Please note that all accepted papers are professionally typeset; the template is intended only as a guideline for author convenience.

    The SPIE journal template is now available in the Overleaf authoring tool. Originally developed to simplify LaTeX authorship, this free online tool has numerous benefits, including:

• real-time collaboration between authors
• an intuitive user interface
• user support and LaTeX help
• easy document sharing and security options
• real-time preview of formatting and equations
• inline error warnings
• a rich-text mode that will look familiar to collaborators who are more comfortable authoring in Microsoft Word
• quick submission to an SPIE journal by following the link "Submit to SPIE Journals" at the top of the Overleaf template.

The SPIE Journal template on Overleaf also featuers helpful LaTeX tutorials and a free introductory course for authors who are new to Overleaf and LaTeX. If you encounter any problems using the SPIE LaTeX template on Overleaf, please contact their support team via https://www.overleaf.com/contact and they will help you resolve the issue.

Artwork Preparation

For peer review, manuscripts should be submitted with the figures/tables and their captions incorporated into the same file as the manuscript text. However, upon first revision or acceptance, authors will be asked to submit individual figure files and a properly formatted manuscript for use in production. The total combined limit for submission files is ~100 MB

Figures must be submitted via the online submission system in EPS, TIFF, PNG, or PDF format. We cannot accept application files, i.e., Corel Draw, Microsoft Word, etc. Number all figures in the order that they appear in the text. All figure parts/panels must be labeled (a), (b), etc. Submit high-resolution figures. The quality of the published figure is only as good as the original file—it cannot be improved by the typesetter.

Figure Permissions: If the figure is derived from a previously published image, the author must obtain permission from the original copyright holder, who may be the publisher and/or the author. Once permission is granted, the figure caption should include the line "Reproduced with permission, courtesy of [copyright owner]," or the publisher's required copyright statement. Many permissions can be obtained via the Copyright Clearance Center .

Figure Requirements:

Tables

Tables should be built in Word, Excel (embedded in Word), or LaTeX. They should not contain graphics. Tables containing images must be numbered as figures. Colored fonts will not appear in the typeset version, so bold and italic should be used for emphasis instead. Explain use of bold or italic in the caption or table footnote. Do not use shading. Very large tables may be vertically oriented, or they may span multiple typeset pages. A caption must be included with the table.

Video

Research articles, letters, and reviews may include video files. Acceptable file formats, including MOV, MPG, and MP4, are playable using standard media players, such as VLC or Windows Media Player. Standard media players should be used to check file properties and image/sound quality prior to submission. Because the speed of internet connection varies, a recommended maximum size for each video file is approximately 12 MB.

The video should be mentioned according to the following numbering convention: Video 1, Video 2, etc. If videos are included as part of an existing figure, they should be described and identified within the figure caption. The media file type and size should be included in parentheses at the end of the caption; e.g., (MPEG, 2.5 MB). For example:

Fig. 1 Confocal microscopic images of red blood cells in (a) an isotonic buffer (Video 1) and (b) a hypertonic buffer (Video 2) in three different viewing projections (Video 1, MPEG, 3.1 MB; Video 2, MPEG, 4.2 MB).

Authors are encouraged to provide a representative still image for any stand-alone video. This image should be treated as a figure, numbered in sequence, and submitted in one of the accepted figure file formats. A caption describing the content of the video file is required, similar to a typical figure caption. For example:

Fig. 4 Photodynamic therapy response of the targeted region (MP4, 5 MB).

Code and Data

In support of open scientific exchange, SPIE journals require Code and Data Availability statements in all accepted papers. These statements should describe how to access any data that would be required to replicate or interpret the findings reported in the paper. Authors are encouraged to make the data and code related to the manuscript publicly available whenever possible, utilizing repositories that are well-known to the field (FigShare, Github, CodeOcean, etc.).

Availability Statement

If the data or code cannot be made publicly available, authors should state the reason and explain how it can be obtained. Likewise, if data sharing is not applicable, the statement must say so.

The following examples may be used as guidance for Data Availability Statements:

• All data in support of the findings of this paper are available within the article or as supplementary material.
• The data presented in this article are publicly available in [repository name] at [DOI link].
• The archived version of the code described in this manuscript can be freely accessed through Code Ocean [DOI link].
• The data utilized in this study were obtained from [third party name]. Data are available from the authors upon request, and with permission from [third party].
• The data that support the findings of this article are not publicly available due to [privacy, ethical concerns]. They can be requested from the author at [email address].
• Data sharing is not applicable to this article, as no new data were created or analyzed.

Repositories

Code and data can be shared using any well-known repositories, including FigShare, Github, and CodeOcean. Data or code contained in an external repository should be cited in the reference list, and authors should include a DOI whenever it is available.

Dataset Reference Example: Creator Name, “Dataset Title,” Repository Name, version (publication year). https://doi.org/.....

Manuscripts that include externally hosted code should mention that code and the name of the repository in the text of the paper or figure caption:

Example 1:
The archived version of the code can be freely accessed and executed through Code Ocean.  

Example 2:
The code used to generate the results and figures is available in a Github repository.

Code Ocean is SPIE's recommended platform for sharing code, but other repositories may be similarly used as a hosting platform. Software and code essential for reproducibility and reuse can be easily incorporated into your SPIE journal manuscript via Code Ocean.

If you intend to upload code to Code Ocean, you may do so before or after article acceptance, but prior to publication. Authors of papers that mention code/software on Code Ocean will receive instructions on how to link the code to the article in the author proofs.

Disclosures

Conflicts of interest include relationships, affiliations, and financial interests pertinent to the research presented in a manuscript. Potential conflicts of interest may include employment, ownership of stock or stock options, patents, honoraria, grants, royalties, consultancies, donations, and other types of funding. Even the appearance of a conflict can constitute a breach of ethical publishing, and therefore situations and activities that may be perceived as conflicts should be reported. Conflict of interest disclosures should cover the past three years.

If no conflicts of interest exist, a statement confirming “The authors declare that there are no financial interests, commercial affiliations, or other potential conflicts of interest that could have influenced the objectivity of this research or the writing of this paper” is included in a Disclosures section of the manuscript.

Supplementary Material

Authors may submit supplementary material supporting original research articles. Please indicate whether the supplementary material is intended for publication. 

If intended for publication, supplementary material such as notes, figures, and tables should be compiled by the author into a single "Supplementary Material" PDF, to be linked to the parent article upon publication (e.g., doi  10.1117/1.NPh.6.2.025014.s01). 

Countable supplementary items mentioned in the primary text should be numbered sequentially with an uppercase S to identify them as supplementary, i.e. Figure S1, Figure S2, etc. 

References cited in the supplementary material must be included in the full list of references in the main article; if any references are not cited in the main text, they should be listed in order at the end of the main reference list.

Other types of supplementary material (e.g., Excel data spreadsheet) may be considered for publication, if they will benefit the reader's understanding of the work. Please contact editorial staff at neurophotonics@spie.org for guidance.

All supplementary material will be assessed for appropriateness and value as supporting information to the submitted manuscript. The journal editor has final authority to decide whether supplementary material should be published with the article. Authors are responsible for ensuring that any supplemental materials they submit are not subject to any prior copyright.

Peer Review Process

All submissions are screened to ensure they meet basic standards of manuscript presentation and are also processed through Crossref Similarity Check. Manuscripts are then evaluated by the editor-in-chief (EiC) and/or a designated editorial board member (EBM) to ensure they meet the journal's rigorous scientific standards and are eligible for peer review. Manuscripts that meet these criteria are reviewed (single-anonymous) by at least two referees selected by the EBM based on their expertise in the topic. The referees provide detailed comments and recommendations to help the EBM arrive at the appropriate editorial decision. Revised manuscripts are evaluated by the EBM and are sent back to the original referees in the case of major revisions. The EiC has the ultimate authority to accept or reject a submission.

Authors may appeal to the EBM or EiC to reconsider a rejection decision if they believe that the reviewers have seriously misjudged the manuscript. All appeals will be given careful consideration. The EBM and/or EiC will determine if further consideration is merited or if the original decision should stand.

Submissions from editors or members of the editorial board are handled by an editorial board member who is not connected with the manuscript to ensure that such submissions receive an objective and unbiased evaluation. Information about the review process for such submissions is redacted from the view of any editors or editorial board members who are authors of the paper within the journal's online submission and review system.

Open Access

Neurophotonics became a fully open access journal in January 2019. Papers are published under a Creative Commons license. Authors of accepted papers are required to pay an article processing charge (APC) of $1675. SPIE members, authors at SPIE Digital Library subscribing institutions, and authors from special economic consideration nations are eligible for APC discounts.  Read more about the fee, discounts, and license for open access publication.

Copyright and Licensing

As of January 2019, Neurophotonics papers are published under a Creative Commons Attribution license (CC BY 4.0). Upon acceptance, authors are given instructions for completing and returning the CC BY license form. 

Under the CC BY license, ownership of copyright in the article (if applicable) and all other proprietary rights, including patent rights, remain with the author(s). In addition to any rights under copyright, the author(s) retain the rights (a) to reproduce, distribute, and publicly display the article in any form or medium; (b) to prepare derivative works from the article; and (c) to authorize others to make any use of the article, provided that proper full attribution is given to the original SPIE publication.

Author Proofs

Accepted papers are immediately sent into production, where they are professionally copyedited and typeset in XML. It usually takes 10-12 days after acceptance to generate the first proof. The corresponding author will be notified by email when the proof is ready to review. Changes should be kept to a minimum. Additions or subtractions of large portions of text may require re-review, and numerous changes may incur article processing charges.

Promote Your Research

A research project doesn't end with publication of a journal paper. It's up to the researcher to share that project through various channels of science communication in order to expand the audience from a small group of academic peers to the wider public. These efforts are important for building public trust in science, and may even foster connections with future funders, collaborators, or employers.

Here are some ways you can publicize your new article:

• Share your article on social media. This tip sheet for SPIE journal authors can help get you started.
• Write an article summary to share with your institution’s communications or PR office, or commission Impact Science to write one for you with SPIE’s Enhanced Article Processing Charges (APCs).
• Update your online CV and website to include a complete citation to the article.
• Inform your institution that it has been published so that it may be added to any lists of publications they maintain and disseminate.
• Create a 90-second Explainer Video to be published with your paper and shared on social media.

How to Cite

SPIE Journals use six-digit citation identifiers (CIDs) in place of traditional page numbering. This allows an issue to build online one article at a time, while retaining the ability to segment tables of contents by article type or subject area. An example of the correct citation format for an Optical Engineering article is:

A. Smith and B. Jones, "Paper title," Opt. Eng. 44(2), 023407 (2005).

In this fictitious example, the article by Smith and Jones was published in Optical Engineering in Issue 2 of Volume 44, as the seventh article published under section category 34.

In the full-text PDF file available online and in the printed article, the CID appears on each printed page. Appended at the end of the CID is a hyphen followed by a consecutive page number. For the sample article above, the printed pages would carry this page numbering: 023407-1, 023407-2, 023407-3, etc. The hyphen and additional digits should not be used when citing or searching for an article.

Article Sharing

For details about publication licenses and the associated rights to share published articles, see the SPIE policies on article-sharing.

Corrections and Retractions

As a publisher, SPIE has an obligation to maintain the integrity of the scholarly record, and will make changes to published articles in certain circumstances, as described here.

Errata

An erratum describes corrections to a published paper resulting from errors with data or interpretation, omissions of information, or any other technical error. An erratum may be initiated by the author, a reader, or an editor, but must have the author’s approval. These statements are published separately from the original paper and include a citation to the original article. When an erratum is published, the original work will also, whenever possible, be corrected and republished with a Corrected date on the PDF, which helps to prevent future duplication of the error.

Any changes to the author list post-publication require approval from all authors and the Editor in Chief, and are at the discretion of the Publisher.

Errata are free to read.

Publisher’s Note

When an error in a paper is initiated by the publisher, such as something inadvertently introduced during copyediting or typesetting, and the error impacts the integrity of the article, a Publisher’s Note may be issued. In this case, the original article will be corrected and republished online with a Corrected date on the PDF. The Publisher’s Note will describe the change and include a citation and link to the original article. Publisher’s Notes are free to read.

Retraction

Retractions can be initiated by a journal editor, author, publisher, or an author’s institution. The journal editor may consider retraction if they have clear evidence that the paper’s findings are unreliable, either as a result of a major error, or as a result of fabrication or falsification. Other reasons for retraction include plagiarism; previously reported findings, without proper attribution; unauthorized data or material; copyright infringement; unethical research involving human or animal subjects; work published solely on the basis of a compromised or manipulated peer review process; the authors failed to disclose a significant conflict of interest; or egregious dishonesty surrounding authorship, including paid authorship or listing authors without their permission. These reasons for retraction are in line with the Council of Publication Ethics (COPE) guidelines on retraction.

In the case of retraction, the PDF of the original paper will be republished with a “Retracted” watermark across all pages, and the word “Retracted” will be added to the paper title. The online version of the article will be replaced by a retraction notice that includes the full citation of the original paper and the reason the paper is retracted. The retraction notice will effectively replace the original paper, with the same DOI and citation information.

Prior to retraction, authors will be given an opportunity to respond and appeal, but retraction does not require unanimous agreement of the authors. Retraction notices are free to read.

Name Changes

SPIE allows authors to change their names in support of diversity, equity, and inclusion in research communities. Authors may wish to change a name due to gender identity, marriage, divorce, religion, or other reasons, and SPIE will not require proof or supporting documentation for this change. When an author requests a name change on a work or works published in the SPIE Digital Library, the paper(s) will be updated and republished online, while maintaining the same citation information. Name changes do not require an erratum. It is recommended that co-authors are informed of the name change.

Misspellings and errors in an author's name are a different matter and still require correction via erratum.

To request a name change, please contact name_change_request@spie.org with your request. Include the paper DOI and the name change information. We will update the paper promptly and republish online, which will trigger it to be redelivered to all abstracting and indexing databases.

Misuse of this policy is an ethical violation and will be investigated and acted upon.