Overview

Overview

Publishing in Elemental Microscopy (EM) provides a groundbreaking way to share experimental data through highly interactive figures and dynamic content. EM is built for researchers who want to go beyond static PDFs, offering tools to publish open-access articles that integrate data, code, and multimedia while promoting transparency, reproducibility, and innovative publishing tools.

Publication in EM is currently free, though we will be introducting an APC in 2026.


Interactivity

One of the most significant advantages of publishing in Elemental Microscopy is the ability to include interactive figures:

  • Images: Readers can zoom in, adjust contrast, flip between raw and processed data channels, overlay information, and customize colormaps.
  • Movies: Embed movies directly within your manuscript, enabling readers to adjust playback speed, view live analyses, or interact with annotations in real time.
  • Plotting data: Add plots that allow readers to expand visualizations, explore statistics, view error bars, and compare data across multiple channels interactively.
  • 3D volumes: Incorporate volumetric data with tools to control viewing angles, magnifications, slice positions, and isosurface levels, making complex datasets more accessible.
  • Anything else you can imagine: You can include any python or jupyter tools you have developed for your research directly in your articles.

Interactivity can make your research more engaging and enable readers to explore your science in unprecedented depth.


Code

Elemental Microscopy is built on the Jupyter Book publishing platform and MyST Markdown typesetting language, allowing seamless integration of Jupyter notebooks. Authors can:

  • Reproduce workflows for visualization, analysis, and simulation directly in the article.
  • Save time by publishing pre-existing Jupyter notebooks without needing to reformat them into LaTeX or Word.
  • Embed executable code snippets that readers can run, fostering deeper engagement with your work.

This approach eliminates tedious reformatting and promotes transparent, reproducible research.


Flexibility

With flexible article lengths, EM supports diverse contributions:

  • Detailed tutorials and reviews.
  • In-depth explorations of methodologies.
  • Compact studies focusing on specific microscopy techniques.

Authors have the freedom to adapt the scope of their articles to meet the needs of the microscopy community.


Preprints and Peer Review

Elemental Microscopy supports an open preprint and peer review model:

  • Preprints: Publish a draft version of your article with a “preprint” label to solicit community feedback.
  • Peer Review: Articles undergo an open peer review process. Reviewer comments are published alongside the article, ensuring transparency and accountability. Reviewers can choose to remain anonymous or disclose their identities.

Accepted articles have the “preprint” label removed, with all referee reports permanently attached, offering a clear record of the review process.


Open Access

All articles in EM are published under the CC BY 4.0 license, ensuring:

  • Open Access: Articles are freely available for anyone to read, share, and reuse.
  • Transparency: Inline links to raw data, code repositories, and supporting materials make your research fully reproducible.
  • Author Rights: Authors retain copyright over their work.

This model aligns with the principles of open science and maximizes the impact of your research.


How to Get Started

Ready to submit your article or want to learn more? Visit elementalmicroscopy.com or contact the editorial team:

We look forward to helping you publish cutting-edge, interactive microscopy research with EM!