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, how it was used, and the prompts that were 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:
File types |
EPS, TIFF, PNG, PDF, or PS |
Dimensions |
Figures will be reduced to a maximum width of 3 and 5/16 in. for two-column layout, and a maximum width of 6 and 3/4 in. for single-column layout. |
Background |
Avoid graphs with shaded, transparent, or grid backgrounds. The background should be white. |
Colored lines |
All line art should be distinguishable in grayscale. If colored lines are used, please add symbols or dot-dash textures to distinguish lines in all graphs. |
Line weight |
Ensure that line weights will be 0.5 points or greater in the final published size. Light-colored lines do not show up when printed in grayscale. |
Alpha channel |
No |
Compression |
LZW with .tiff files |
Resolution |
300-600 pixels per inch (ppi). Enlarge to 150% to check for jagged or blurry lines, indicating low resolution. |
Layers |
Flattened, no layers |
Color mode |
RGB or CMYK |
Text |
No smaller than 8 pt. Use a clear and readable font such as Times, Arial, or Symbol. |
Captions |
Do not include in image file. Captions should be listed separately within the manuscript and contain descriptions of all labeled figure parts (a), (b), etc. |
File size |
Maximum of approximately 3 MB per figure |
Multipart figures |
All parts should be included in one file, on one page. For example, if Figure 1 contains three parts (a, b, c), then all of the labeled parts should be combined in a single file for Figure 1. |
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.