Author Instructions

We recommend printing these guidelines so they can be consulted throughout the submission process.

Author Guidelines
Before proceeding, please click here to read the policies and author guidelines on the SPIE website.

*Please note that our submission form has changed to a tabbed view format.*

File Formats
Manuscript materials must be submitted to the journal as follows:

If a manuscript is being submitted for initial peer review, you will need to upload a single, complete manuscript file that contains both the article text (including references, tables, and captions) AND the figures (either within the manuscript near each figure callout, or grouped at the end). The source file should be in one of the following formats: Word, PDF, PS, or LaTeX/REVTeX format. Your uploaded source file will be converted to PDF format, which will be used for the review process.

Note that if the Associate Editor’s decision of your manuscript requires revision, you will then be requested to supply individual figure files in one of the following source file formats: TIFF, PS, EPS, or PDF. Authors of accepted manuscripts are required to have submitted their individual figures before their manuscript can move forward into Production. Upload any multimedia files separately. See multimedia guidelines below.

Please note: Prior to acceptance, if your manuscript is not formatted correctly, you will be required to submit a manuscript that is properly formatted for Production.

Manuscript Formatting Guidelines

• Manuscript pages should be numbered.
• The entire manuscript must be double-spaced, including the abstract and references (do not use single or 1.5 line spacing).
• Please do not use acronyms in the title or keywords; all acronyms should be spelled out at first use.
• The manuscript should be ordered as follows: title page, abstract, text, acknowledgments, references, tables, list of figure captions. Note: Table captions may remain with the tables; however, a double-spaced list of figure captions must be included at the end of the manuscript’s text (for initial peer review, the figure captions may be included with the figures themselves).
• Preferably, the article text file should be submitted in Microsoft Word. (Alternatively, the article text may be submitted in PDF; however, note that this format is not usable for composition.)
• For LaTeX and RevTeX users: Submit a complete manuscript (as noted in above “File Formats” section) in LaTeX or RevTeX. File should be a single .tex file. Multiple-file submissions are not supported. Figure files may be called in. Submission of .sty files or .bib files is not supported. Submissions in Plain TeX format or in dvi format are not supported.
• For Microsoft Word submissions: Do not enter a paragraph mark or hard return at the end of each line of text, since this may cause conversion problems. Hard returns or paragraph marks should only be entered at the end of a paragraph.

See additional manuscript formatting guidelines here.

Figure Preparation Guidelines
It is important that the following instructions be followed precisely for the graphics files to be utilized in the journal production process.

• For initial peer review, figures should be included in the article file, either near the figure callouts or grouped at the end of the manuscript. However, for revised manuscripts, authors must provide individual figure files in TIFF, PostScript, EPS, or PDF. This will ensure optimal quality of figures in the final published article.
• We can accept PostScript (PS), Encapsulated PostScript (EPS, using either Arial or Times Roman fonts), TIFF (lzw compressed), or PDF figure files. We cannot accept application files, i.e., Corel Draw, Microsoft Word, PowerPoint, etc.
• Make sure there is only ONE figure per file. Each figure file should contain all parts of the figure. For example, if Figure 1 contains three parts, (a), (b), and (c), then all of the labeled parts should be combined in a single file for Figure 1. Do not upload multiple page figure files.
• Figure part labels [(a), (b), (c), etc.] should be included in the file; a font size of 8 points for the labels is preferable.
• Figures should be numbered consecutively (not by section).
• Set the graphic for 600 dpi resolution for line art, 264 dpi for halftones, and 600 dpi for combinations (line art + halftone).
• Submit color files at 300 dpi TIFF, PS, or EPS format. If selecting a file mode, use CMYK (Cyan, Magenta, Yellow, Black) or RGB (Red, Green, Blue).
• Save line art as black/white bitmap; not grayscale.
• Save halftones and combinations as grayscale, not black/white bitmap.
• Set the bounding box to image to avoid excess white space around the image.
• Submit ALL illustrations for each article, including line art.
• If possible, size your illustrations according to the journal's specifications for column widths: 3 & 5/16 inches (20 picas) for one column, and 7 inches (42 picas) for two columns. Submit each illustration at the final size in which you would like it to appear in the journal. Each illustration should be prepared for 100% reproduction.
• Avoid submitting illustrations containing small axes with oversized labels.
• Ensure that line weights will be 0.5 points or greater in the final published size. Line weights below 0.5 points will reproduce poorly.
• The graphic should be sent with the correct orientation.
• Check files for extraneous information. Edit out any figure captions or e-mail headers. The only data in the file should be the figure itself.

Multimedia Guidelines
Multimedia files must be submitted as an integral part of the paper. Supplemental multimedia material is not accepted.

See the detailed multimedia guidelines given in the instructions for how to prepare a manuscript. Acceptable file formats for video include QuickTime nonstreaming video (.qt or .mov), MPEG (.mpg), and DV (.dv). Acceptable file formats for audio include PCM (.pcm), WAV (.wav), AIFF (.aif), and MP3 (.mp3) at 128 Kbs or greater. We cannot accept any other types of multimedia files. Please note that AVI files are no longer a recommended file format, because the wide variety of AVI codecs cannot be reliably archived. Authors must also provide a separate representative "still" image taken from the video. This still image is not intended to convey meaning about the content of the video; rather it will be used as a static representation of the video file, which will be linked by the publisher after acceptance. Care should be taken to extract an image from the video which has reasonable clarity of fine lines and details. Acceptable file formats for still images are TIFF, EPS, PS, or PDF.

Manuscript Types

• Regular Paper: A full-length manuscript presenting original work intended as a regular contribution to the journal.
• Regular Paper - Based on SPIE Proceedings Paper: A full-length article presenting original work that is based on an SPIE Proceedings paper. If your manuscript is a revised version of a report previously published in an SPIE conference proceedings, please indicate the volume and paper number and briefly describe the changes made to the paper in the Manuscript Type Comment box located in this section.
• Special Section Paper: A full-length manuscript presenting original work intended for submission to a special topical section organized by a guest editor(s).
• Special Section Paper - Based on SPIE Proceedings Paper: A full-length article presenting original work intended for submission to a special topical section that is based on an SPIE Proceedings paper. If your manuscript is a revised version of a report previously published in an SPIE conference proceedings, please indicate the volume and paper number and briefly describe the changes made to the paper in the Manuscript Type Comment box located in this section.
• Letter: A short technical communication of significant interest intended for rapid publication in the Letters section of the journal. The manuscript length may not exceed three printed journal pages. This corresponds to approximately 3000 words; figures will further reduce the maximum word content. A brief cover letter setting forth the significance of the paper and why it merits rapid publication must be submitted with the manuscript. Letters will be reviewed with the same rigor as regular journal articles but with an accelerated pace.
• Communication: A short technical communication on original work, a comment on a recent paper, or an erratum.
• Review Paper: An article reviewing a particular topic or field. Review papers are typically invited papers written by a highly regarded expert in the field. An author interested in submitting a review paper should submit an abstract and outline of the projected paper to the Editor for approval.
• Technical Notes Paper: A concise description of a software package, instrument, chemical, or procedure that provides a solution to a specific problem but has sufficient value to many readers of the Journal of Biomedical Optics. The Note should occupy no more than five printed pages in the Journal

Cover Letter
A cover letter file is required. The cover letter will not be accessible to the reviewers; it is accessible only to Editors and Staff. In the cover letter, authors should explain the significance of the work, the problem that is being addressed, and why the manuscript belongs in this journal. The cover letter should also contain any pertinent information regarding your submission. If you are submitting a Letters manuscript (which is a short technical communication intended for rapid publication), you must include a statement in the cover letter file setting forth the significance of the paper and why it merits rapid publication.

Submission Process
Please note that our submission form has changed to a tabbed view format. There are now four steps (listed below) to follow in order to complete your manuscript submission. You may choose the order in which you complete the steps, but you must go through all of the steps. Tabs are displayed in each step (click on a tab in order for the required information to be displayed). At any time during the submission process, you may interrupt the upload by clicking on "Save and Exit". When you return, you may continue the interrupted (halted) submission.

File Requirement for Initial Peer Review:
Upload a single, complete manuscript file that contains both the article text (including references, tables, and captions) AND the figures (either within the manuscript near each figure callout, or grouped at the end). The source file should be in one of the following formats: Word, PDF, PS, or LaTeX format. Your uploaded source file will be converted to PDF format, which will be used for the review process.

File Requirements for Revised Manuscripts:
Upload separate files (i.e. Response to Reviewer Comments file, Article file, Figure file(s), and Multimedia files). You will select files to upload one at a time. When you have finished, click on "Upload Files" to transfer the selected files to the journal website. If you find that you have made a mistake after uploading the files, you may click on "Remove Files" or "Replace Files" to make changes. Also, you may remove files at various steps in the submission process.

1. Choose a "File Type" for each file that you are uploading. The categories are self-explanatory (for instance, "article file" will be the text of the manuscript; "figure" a figure, etc.).
2. Make sure there is only ONE figure per file. Each figure file should contain all parts of the figure. For example, if Figure 1 contains three parts, (a), (b), and (c), then all of the labeled parts should be combined in a single file for Figure 1. Do not upload multiple page figure files.
3. Figure files will also require an additional step where you identify them (e.g., "Figure 1").
4. Place the files in order. The files will appear in a box ordered according to their file type and identification. If some of the files require re-ordering, you may drag and drop the files until they are in the proper sequence. Or, you may change the sequence of a single file by typing its proper sequence number in the text box to the left of the file and then click out of the text box.

Step 2: Manuscript Information (overview of tabs in Step 2):

Manuscript Type: Select your manuscript type (i.e. Regular Paper, Special Section Paper, etc.).

Title, Abstract: In the appropriate boxes, type in the manuscript title, and the abstract of the article. Please use ASCII text. The abstract will be sent to the referees whom the editors contact about reviewing the paper. By the side of each box is a table of symbols that you may use to insert non-ASCII symbols. The abstract is a summary of the paper and not an introduction. The maximum allowable length of an abstract is 200 words. Because the abstract may be used in abstracting journals, it should be self-contained (i.e., no numerical references) and substantive in nature, presenting concisely the objectives, methodology used, results obtained, and their significance.

Authors: Type in the information for the corresponding author. Each field marked with an asterisk (*) is required. All required fields must be completed. If there isn’t available information for a particular field, please indicate so (e.g., "Telephone: no phone"). You must type in information for each of the other authors.

Index Terms and Category: Choose at least three index terms and indicate the category where you believe your paper belongs.

Detailed Information: Required information regarding your manuscript.

Page Charge Agreement: Information to be completed regarding Page Charges.

Author Editor and Reviewer Suggestions: You have the option to suggest four (4) possible reviewers who are knowledgeable about the topic of your paper but who are not affiliated with your current research and are not on the Editorial Board. These suggestions will be used at the Associate Editor's discretion.

Step 3: Confirm Manuscript: Confirm your uploaded file(s) and manuscript data. Errors will be indicated with red lettering and a link to the screen where the error can be fixed (error will be indicated with a large red arrow).

Step 4: Submit Manuscript:

1. When your manuscript is ready to be submitted, click on the “Approve Submission” button to complete your manuscript submission. Once your manuscript has been submitted, you may not alter it.
2. Upon confirming approval of the converted files, you are returned to your Home screen (Main page) with a message indicating that the submission has been registered. You now have the opportunity to view summary data, converted files, and current status information about your manuscript by checking the "Live Manuscripts" folder.

NOTE: Until you complete “Submit Manuscript" (Step 4), your manuscript is not considered as submitted to the editorial office for peer-review handling.

Quality Check of Submission by Editorial Office
Upon receiving system notification of a submission, the journal Staff will check to make sure the manuscript submission is complete and that the files are properly prepared. If the submission is ready to be processed, the Author will receive a "confirmation of receipt" email message and the submission passes to the Editor. If the journal Staff has any questions or needs additional information, the Author will receive a "quality check" email message with a description of what is needed and instructions for amending the submission and/or supplying additional information.

Revised Manuscript Submissions
The process for submitting a revised manuscript proceeds through the same series of screens as before. However, there are some important differences.

1. The previously submitted data from your original manuscript submission form is presented and can be edited.
2. The files from the previous manuscript will be "copied forward" for the revised version. These files will be presented to you for replacement, deletion, or addition of a file on one of the screens after the submission-form screen. Replace the original article file with your revised manuscript. Do not resubmit your original manuscript. You are required to add a Response to Reviewer Comments file.
3. Please submit your individual figure files at this time. Figures should be removed from the article file when submitting a revision. (see Step 1. “Submitting Revised Manuscript Files” for details).

Please double check to make sure that each uploaded file is the most current version.

Publication Charges
Publication charges of $90 per published page apply to both contributed and special section papers. Editorial acceptance of papers is not tied to payment of publication charges, but such payments are expected. These charges are financial contributions from authors' institutions to help defray the cost of publishing research results and should be regarded as an essential and proper part of their research budgets.

For authors who pay the voluntary page charges of $90 per published page in full, papers will become open access 12 months after the date of publication. This policy became effective as of the September/October 2009 issue of JBO. This option is not available to authors who have published in prior issues of JBO.

Open Access Option: SPIE offers authors the option to pay a fee of $1500 to support publication costs and to provide free online access to the full text of their published journal article, in perpetuity, to any online user, independent of any subscriptions to the journal. To select open access, please return the Open Access Publication Form with payment to SPIE either before or at the time you return your author proof corrections.

Open access to the article can be ensured only if payment in full is received by SPIE before the author’s proof corrections are completed. An author’s choice to select open access has no impact on any aspect of the peer-review process or on the Editor’s ultimate decision regarding publication. If an author chooses open access, but SPIE does not receive full payment before completion of the author corrections, the article will be published conventionally, that is, without open access. Payment of the open access fee covers regular page charges but does NOT cover other publication charges, such as charges for reprints or color printing.

Color Figures
Authors or their sponsors must bear the cost of printing in color. Upon acceptance, the Editorial Office will provide the author with information about color figure preparation and cost. Alternatively, color is free for authors who choose to have color only in the online version of the journal. To take advantage of this option, authors must provide the figures in the proper electronic format. The journal reserves the right to publish figures in black and white online if the electronic figures are unusable or are received too late in the production process. For more information, click here or contact the Editorial Office.

Copyright Transfer Agreement
The Transfer of Copyright Form must be completed and returned prior to publication of an accepted article. The form is available via a link in the navigation bar at the bottom of the pages of this site.

Download the copyright form, print it, complete it in full (include manuscript code number and journal name), sign it, and mail, fax, or email it to the Editorial Office as soon as you are notified that your article has been accepted for publication.

Navigation and Getting Help
The upper right-hand corner of every screen has links that allow you to:

• Return to your Home screen, "Return to Main Page"
• Access a "Suggestions" feedback form
• Access a "Help" contact list
• "Log out" of the journal's Peer X-Press service

Throughout the system, red arrows reflect pending action items that you should address by clicking on the associated link.

If you need additional help, you can click on the help signs located throughout the system. A help dialog box will pop up with context-sensitive help comments.

Checking a Manuscript's Status: Viewing Manuscript Files
After you have approved the file upload and conversion for your manuscript submission, you may obtain the status of your manuscript, or view the manuscript files, at any time:

• Log into the system with your user name and password. The site's URL is http://jbo.peerx-press.org/ . (If needed, use the "Unknown/Forgotten Password" link at the Welcome/Login screen to be emailed your login name and a new, temporary password.)
• Click on the "Live Manuscripts" or "Post Decision Manuscripts" folder, under Author Tasks on your Home screen (Main page).
• Then click on the "Check Status #..." link which takes you to the Detailed Status Information screen.
• In the Detailed Status Information screen, you can click on the link beside the “Manuscript #” to view the files that have been uploaded, approved, and submitted.

Sending Manuscript Correspondence
To send email to the journal staff regarding a manuscript that has already been submitted and is being processed, please use the "Send Manuscript Correspondence" link located at the end of the Detailed Status Information screen. This feature allows you to send email attachments and to cc: (e.g., to yourself). Your email is automatically recorded and stored within the system and accessible to journal staff. An author might use this feature to send in a corrected file for a recently submitted manuscript (provided the editorial process has not yet progressed too far).

Starting the Process
Start the manuscript submission process by clicking the "Submit Manuscript" link on your Home screen (Main page).

Return to Main Page to continue.