From 7e833cb8904eb3ea65eba3d03940427d940f945c Mon Sep 17 00:00:00 2001 From: cophus Date: Sat, 25 Jan 2025 15:36:33 -0800 Subject: [PATCH 01/10] Various updates --- editors.md | 14 +++-- index.md | 2 +- overview.md | 79 ++++++++++++++++++++----- writing-an-article.md | 132 +++++++++++++++++++++++++++++++++++++++++- 4 files changed, 204 insertions(+), 23 deletions(-) diff --git a/editors.md b/editors.md index f5199a6..c8e2675 100644 --- a/editors.md +++ b/editors.md @@ -3,19 +3,21 @@ title: Editors and Developers description: Elemental Microscopy is headed up by Editor-in-Chief, Colin Ophus and is part of the Microscopy Society of America. --- -## Editor-in-Chief +## Editors -`Colin Ophus` is a staff scientist at NCEM, part of the [Molecular Foundry](https://foundry.lbl.gov/), at [Lawrence Berkeley Lab](https://www.lbl.gov/). He runs both a research group and user program focused on methods, algorithms, and codes for simulation, analysis and instrument design for STEM and TEM. He has received a US DOE Early Career award (2018) and was awarded the [Burton Medal](https://www.microscopy.org/awards/bios/burton_physical_2022.cfm) from the Microscopy Society of America (2022). He is project leader for the [Prismatic](https://prism-em.com/) STEM simulation and [py4DSTEM](https://github.com/py4dstem/py4DSTEM) open-source codes. (cophus@gmail.com) +`Colin Ophus` is an [Associate Professor](https://colab.stanford.edu/people) in the [Department of Materials Science and Engineering](https://mse.stanford.edu/) at [Stanford University](https://www.stanford.edu/), and a Center Fellow at the [Precourt Institute for Energy](https://energy.stanford.edu/). He was formerly a staff scientist at the [National Center for Electron Microscopy](https://foundry.lbl.gov/about/facilities/the-national-center-for-electron-microscopy-ncem/), part of the [Molecular Foundry](https://foundry.lbl.gov/), at [Lawrence Berkeley National Lab](https://www.lbl.gov/). He researchs experimental methods, reconstruction algorithms, and data analysis for TEM. He has received a US DOE Early Career award (2018) and was awarded the [Burton Medal](https://www.microscopy.org/awards/bios/burton_physical_2022.cfm) from the Microscopy Society of America (2022). He is project leader for the [Prismatic](https://prism-em.com/) STEM simulation and [py4DSTEM](https://github.com/py4dstem/py4DSTEM) open-source codes. He is the founding editor-in-chief for `Elemental Microscopy`. (cophus@stanford.edu) -## Editorial Board -`Beth Dickey` is the Department Head and Teddy and Wilton Hawkins Distinguished Professor of the [Materials Science and Engineering](https://www.mse.engineering.cmu.edu/index.html) department at [Carnegie Mellon](https://www.cmu.edu/). She is a Fellow of the Microscopy Society of America and of the American Ceramic Society, and is a member of the World Academy of Ceramics. (ecdickey@cmu.edu) +`Georgios Varnavides` is a Miller Fellow postdoc working at the University of California, Berkeley and Lawrence Berkeley National Lab. He is the technology editor for `Elemental Microscopy`. (gvarnavides@berkeley.edu) + + +## Editorial Board -`Georgios Varnavides` is a Miller Fellow postdoc working at the University of California, Berkeley and Lawrence Berkeley National Lab. (gvarnavides@berkeley.edu ) +`Beth Dickey` is the Department Head and Teddy and Wilton Hawkins Distinguished Professor of the [Materials Science and Engineering](https://www.mse.engineering.cmu.edu/index.html) department at [Carnegie Mellon](https://www.cmu.edu/). She is a Fellow of the Microscopy Society of America and of the American Ceramic Society, and is a member of the World Academy of Ceramics. (ecdickey@cmu.edu) -We are currently recruiting additional members of the editorial board! Contact [Colin Ophus](mailto:cophus@gmail.com) if you are interested. +We are currently recruiting additional members of the editorial board! Contact [Colin Ophus](mailto:cophus@stanford.edu) if you are interested. --- diff --git a/index.md b/index.md index c2d3334..0cb6d8f 100644 --- a/index.md +++ b/index.md @@ -5,4 +5,4 @@ description: Elemental Microscopy is an online journal published by the Microsco `Elemental Microscopy` is an online journal published by the [Microscopy Society of America](https://www.microscopy.org/). Our articles are highly interactive, leveraging the power of open-source scientific programming communities, and modern internet technologies. -We will offer review and tutorial treatments of key topics, ranging from fundamental theory, instrumentation advancements, experimental methods and data analysis. These articles offer cutting-edge insights into emerging applications in a variety of areas including **biology**, **life sciences**, **geology**, **engineering**, **materials science**, **nanoscience**, **physics** and **archeology**. With embedded video, interactive code and data content, the publication serve as excellent educational resources for the microscopy and the broader science community. Regularly updated and developed specifically for a digital environment, this journal is a dynamic and enduring reference resource for students, researchers, and practitioners in microscopy. +We offer reviews and tutorial treatments of key topics, ranging from fundamental theory, instrumentation advancements, experimental methods and data analysis. These articles offer cutting-edge insights into emerging applications in a variety of areas including **biology**, **life sciences**, **geology**, **engineering**, **materials science**, **nanoscience**, **physics** and **archeology**. With embedded video, interactive code and data content, the publication serve as excellent educational resources for the microscopy and the broader science community. Regularly updated and developed specifically for a digital environment, this journal is a dynamic and enduring reference resource for students, researchers, and practitioners in microscopy. diff --git a/overview.md b/overview.md index fb9c471..baa58d6 100644 --- a/overview.md +++ b/overview.md @@ -3,33 +3,84 @@ title: Overview description: Publishing in Elemental Microscopy allows you to publish experimental data using highly interactive figures. --- -Interactivity -: One major benefit of publishing in `Elemental Microscopy` is that you can publish experimental data using **highly interactive figures**. These include: -- **Images** where you can zoom in, change the contrast levels, flip between channels such as raw and processed, modify colormaps, and overlay additional information. +## Overview -- **Movies** embedded directly in the text with the ability to play back at any speed, show live analysis, and all of the other interactive options available for images. +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. -- **Plotting Data** which can be expanded to show statistics, sources of input data and error bars, and correlation between channels. +--- + +## 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**, 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. -- **3D Volumes** with control over the viewing direction and magnification, isosurface levels, slice positions, and embedded measurements. +This approach eliminates tedious reformatting and promotes transparent, reproducible research. --- -Code -: Built on the Jupyter Book publishing platform and MyST markdown language, `Elemental Microscopy` articles can include Jupyter notebooks which reproduce visualization, analysis, and simulation workflows. Authors can save time by publishing notebooks directly rather than rewriting into LaTeX or Word formats, and then typesetting into journal-specific formats. +## Flexibility + +With **article lengths ranging from 5,000–30,000 words**, 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. --- -Flexibility -: With lengths of approximately 5,000–30,000 words, `Elemental Microscopy` offer an opportunity to develop a theme in greater detail than is possible in a traditional journal article, yet more concisely than would be expected in a full-length book. +## 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. --- -Preprints and Peer Review -: You can publish the initial version of a scientific paper on the `Elemental Microscopy` platform, marked as a preprint version. EM articles will then go through a peer review process. After passing this review, accepted articles will have the preprint label removed and have all referee reports attached to the paper. Reviewers may opt to publish their names alongside their review, or remain anonymous. +## 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. --- -Open Access -: All `Elemental Microscopy` articles will be published under a CC BY 4.0 open access license. Each article will contain not only the code required to produce all results and figures, but also inline links to raw data and source code repositories. +## How to Get Started + +Ready to submit your article or want to learn more? Visit [elementalmicroscopy.com](https://www.elementalmicroscopy.com) or contact the editorial team: + +- [Colin Ophus](mailto:cophus@stanford.edu), Founding Editor-in-Chief +- [Georgios Varnavides](mailto:gvarnavides@berkeley.edu), Technology Editor + +We look forward to helping you publish cutting-edge, interactive microscopy research with EM! + diff --git a/writing-an-article.md b/writing-an-article.md index 31ebd68..40809c0 100644 --- a/writing-an-article.md +++ b/writing-an-article.md @@ -4,8 +4,136 @@ description: '' short_title: '' --- - ```{important} -The submission process is currently invite only! Please get in touch with [Colin Ophus](mailto:cophus@gmail.com) if you are interested in writing an article for `Elemental Microscopy`. +The submission process is currently invite only! Please get in touch with [Colin](mailto:cophus@stanford.edu) or [George](mailto:gvarnavides@berkeley.edu) if you are interested in writing an article for `Elemental Microscopy`. ``` + +These instructions will help you prepare and submit your manuscript using the EM platform. We give instructions for both advanced and beginning users, based on their familiarity with basic command-line tools, version control using Git, and working within a Python environment. + +The EM platform uses open-source technologies such as MyST Markdown, Jupyter Notebooks, and Conda for environment management. Authors are encouraged to include interactive elements such as embedded code, multimedia (e.g., images, movies, 3D volumes), and datasets in their manuscripts. While advanced technical expertise is not required, familiarity with these tools will help you fully leverage the platform's capabilities. For new users, EM provides templates, documentation, and examples to guide you through the process. Please contact [Colin](mailto:cophus@stanford.edu) or [George](mailto:gvarnavides@berkeley.edu) if you need some help getting started! + +--- + +## Advanced Users + +### Step 1: Setting Up Your Environment + +1. **Clone the Repository** + - Fork the [EM Quickstart](https://github.com/msa-em/em-quickstart), [EM Template](https://github.com/msa-em/em-template), or another EM article from [GitHub](https://github.com/msa-em). + - Clone your fork: + ``` + git clone git@github.com:msa-em/.git + ``` + - Switch to the `dev` branch: + ``` + git checkout dev + ``` + +2. **Configure the Environment** + - Edit the `environment.yml` file: + - Change the environment name to match your repository name. + - Add any required Python package dependencies, pinning versions as needed. + - Create the virtual environment: + ``` + conda env create -f environment.yml + ``` + - If the environment already exists, remove it: + ``` + conda remove -n --all + ``` + - Activate the environment in two terminal windows: + ``` + conda activate + ``` + + +### Step 2: Editing Your Article + +**Modify Configuration Files** + - Edit the `myst.yml` file: + - For local editing, comment out the `jupyter: true` line. + - Uncomment the lines for local Jupyter server configuration: + ```yaml + jupyter: + server: + url: 'http://localhost:8888' + token: '512ac78f14e1141db1fac17e8b4099c1e5bc7d589518b38c' + ``` + +**Run Jupyter and MyST** + - In the first terminal window, start the Jupyter server: + ``` + jupyter lab --IdentityProvider.token=512ac78f14e1141db1fac17e8b4099c1e5bc7d589518b38c --ServerApp.allow_origin='http://localhost:3000' --port=8888 + ``` + - In the second terminal window, start the MyST server: + ``` + myst start + ``` + +**Add Your Article Content** + - Write your manuscript in MyST Markdown, making sure to organize your sections into separate markdown files, and using subsections where appropriate. As you write the article content, embed code, multimedia, and data as needed. + - Remember that when committing your local `myst.yml` changes, you will need to switch back to `jupyter: true` for the web-based version. + + +### Step 3: Previewing and Finalizing + +**Preview Your Article** + - Push your changes to the `dev` branch. + - Open a draft pull request (PR) into the `main` branch. GitHub Actions will deploy a staging site for live previews. + - Click the "Inspect" link in the GitHub Actions bot message to preview your article on the Curvenote staging site. + +**Merge When Ready** + - Once all content is finalized, merge the PR into the `main` branch. Ensure thematic changes are grouped together. + +--- + + +## Beginner Users + +### Getting Started + +If you're new to the tools and processes used for Elemental Microscopy, follow these simpler steps to get started without using GitHub or advanced command-line tools. These instructions will guide you through preparing and submitting your manuscript. + +### Step 1: Download Template + - Choose a template to get started, either: + - The [EM Quickstart Template](https://github.com/msa-em/em-quickstart). + - The [full EM Template](https://github.com/msa-em/em-template). + - The templates includes basic formatting, example figures, and placeholders for multimedia or code. + - Save the template to your computer and open it using any Markdown-compatible editor (e.g., [Sublime](https://www.sublimetext.com/),, [Typora](https://typora.io/), [Visual Studio Code](https://code.visualstudio.com/), or a simple text editor). + +### Step 2: Edit Your Manuscript + - Use the downloaded template to write your article, ensuring you: + - Add clear section headings for organization. + - Insert links or placeholders for multimedia (e.g., images, videos) and datasets. + - Include inline code examples or results, if applicable. + +### Step 3: Interactive Content + - If you want to include interactive visualizations or code, let the editorial team know. They will guide you on how to use pre-configured Jupyter notebooks or help integrate the interactive elements for you. + +### Step 4: Preview Article + - After editing, send your manuscript and associated files (e.g., images, datasets) to the editorial team, either [Colin](mailto:cophus@stanford.edu) or [George](mailto:gvarnavides@berkeley.edu). + - The team will provide a preview link for you to review your draft article on the EM platform. + +### Step 5: Submit for Review + - Once you're satisfied with the draft, the editorial team will guide you through the submission process. + - The article will then go through the open peer review process before publication. + + +### Notes for Beginner Authors + +- **No Installation Required**: Beginner authors do not need to set up a local environment or use GitHub. All technical configurations will be handled by the editorial team. +- **Focus on Content**: Concentrate on the clarity and organization of your article. The editorial team will assist with integrating multimedia and code. + + +--- + + +## Best Practices + +- Use templates and examples provided in the repository to guide your writing. +- Ensure all code blocks are reproducible and include inline comments. +- Cite datasets and code repositories using DOIs where possible. + +For further assistance, please contact the editorial team at [elementalmicroscopy.com](/editors). + From 33168135a09cf7dac02e8b7688730f0dcb52c7e5 Mon Sep 17 00:00:00 2001 From: gvarnavi Date: Sat, 25 Jan 2025 16:33:52 -0800 Subject: [PATCH 02/10] index changes --- index.md | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/index.md b/index.md index 0cb6d8f..3aee50d 100644 --- a/index.md +++ b/index.md @@ -3,6 +3,10 @@ title: Elemental Microscopy description: Elemental Microscopy is an online journal published by the Microscopy Society of America. Our articles are highly interactive, leveraging the power of open-source scientific programming communities, and modern internet technologies. --- -`Elemental Microscopy` is an online journal published by the [Microscopy Society of America](https://www.microscopy.org/). Our articles are highly interactive, leveraging the power of open-source scientific programming communities, and modern internet technologies. +`Elemental Microscopy` is an online journal published by the [Microscopy Society of America](https://www.microscopy.org/). +Our articles are highly interactive, leveraging the power of open-source scientific programming communities, and modern internet technologies. -We offer reviews and tutorial treatments of key topics, ranging from fundamental theory, instrumentation advancements, experimental methods and data analysis. These articles offer cutting-edge insights into emerging applications in a variety of areas including **biology**, **life sciences**, **geology**, **engineering**, **materials science**, **nanoscience**, **physics** and **archeology**. With embedded video, interactive code and data content, the publication serve as excellent educational resources for the microscopy and the broader science community. Regularly updated and developed specifically for a digital environment, this journal is a dynamic and enduring reference resource for students, researchers, and practitioners in microscopy. +We offer reviews and tutorial treatments of key topics, ranging from fundamental theory, instrumentation advancements, experimental methods and data analysis. +These articles offer cutting-edge insights into emerging applications in a variety of areas including **biology**, **life sciences**, **geology**, **engineering**, **materials science**, **nanoscience**, **physics**, and **archeology**. +With embedded video, interactive code, and data content, the publications serve as excellent educational resources for the microscopy and the broader science community. +Regularly updated and developed specifically for a digital environment, this journal is a dynamic and enduring reference resource for students, researchers, and practitioners in microscopy. From c8b599e3e328cab70b89e818d3206dcb0dd9aca2 Mon Sep 17 00:00:00 2001 From: gvarnavi Date: Sat, 25 Jan 2025 16:39:43 -0800 Subject: [PATCH 03/10] overview changes --- overview.md | 51 ++++++++++++++++++++++++++------------------------- 1 file changed, 26 insertions(+), 25 deletions(-) diff --git a/overview.md b/overview.md index baa58d6..38e73a3 100644 --- a/overview.md +++ b/overview.md @@ -6,7 +6,8 @@ description: Publishing in Elemental Microscopy allows you to publish experiment ## 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. +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. --- @@ -14,14 +15,10 @@ Publishing in **Elemental Microscopy (EM)** provides a groundbreaking way to sha 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. - +- **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. @@ -30,11 +27,12 @@ Interactivity can make your research more engaging and enable readers to explore ## Code -`Elemental Microscopy` is built on the **Jupyter Book publishing platform** and **MyST Markdown**, allowing seamless integration of **Jupyter notebooks**. Authors can: +`Elemental Microscopy` is built on the **Jupyter Book publishing platform** and **MyST Markdown**, 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. +- 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. @@ -42,11 +40,11 @@ This approach eliminates tedious reformatting and promotes transparent, reproduc ## Flexibility -With **article lengths ranging from 5,000–30,000 words**, EM supports diverse contributions: +With **flexible article lengths**, EM supports diverse contributions: -- Detailed tutorials and reviews. -- In-depth explorations of methodologies. -- Compact studies focusing on specific microscopy techniques. +- 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. @@ -56,8 +54,10 @@ Authors have the freedom to adapt the scope of their articles to meet the needs `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. +- **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. @@ -67,9 +67,9 @@ Accepted articles have the "preprint" label removed, with all referee reports pe 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. +- **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. @@ -77,10 +77,11 @@ This model aligns with the principles of open science and maximizes the impact o ## How to Get Started -Ready to submit your article or want to learn more? Visit [elementalmicroscopy.com](https://www.elementalmicroscopy.com) or contact the editorial team: +Ready to submit your article or want to learn more? +Visit [elementalmicroscopy.com](https://www.elementalmicroscopy.com) or contact the editorial team: -- [Colin Ophus](mailto:cophus@stanford.edu), Founding Editor-in-Chief -- [Georgios Varnavides](mailto:gvarnavides@berkeley.edu), Technology Editor +- [Colin Ophus](mailto:cophus@stanford.edu), Founding Editor-in-Chief +- [Georgios Varnavides](mailto:gvarnavides@berkeley.edu), Technology Editor We look forward to helping you publish cutting-edge, interactive microscopy research with EM! From 0bf553a3a0346e9b7e8ec5bc8afb524c427f53b7 Mon Sep 17 00:00:00 2001 From: gvarnavi Date: Sat, 25 Jan 2025 16:56:58 -0800 Subject: [PATCH 04/10] submit changes --- writing-an-article.md | 52 ++++++++++++++++++++++++++----------------- 1 file changed, 32 insertions(+), 20 deletions(-) diff --git a/writing-an-article.md b/writing-an-article.md index 40809c0..d0d21f4 100644 --- a/writing-an-article.md +++ b/writing-an-article.md @@ -6,12 +6,18 @@ short_title: '' ```{important} -The submission process is currently invite only! Please get in touch with [Colin](mailto:cophus@stanford.edu) or [George](mailto:gvarnavides@berkeley.edu) if you are interested in writing an article for `Elemental Microscopy`. +The submission process is currently invite only! +Please get in touch with [Colin](mailto:cophus@stanford.edu) or [George](mailto:gvarnavides@berkeley.edu) if you are interested in writing an article for `Elemental Microscopy`. ``` -These instructions will help you prepare and submit your manuscript using the EM platform. We give instructions for both advanced and beginning users, based on their familiarity with basic command-line tools, version control using Git, and working within a Python environment. +These instructions will help you prepare and submit your manuscript using the EM platform. +We give instructions for both advanced and beginning users, based on their familiarity with basic command-line tools, version control using Git, and working within a Python environment. -The EM platform uses open-source technologies such as MyST Markdown, Jupyter Notebooks, and Conda for environment management. Authors are encouraged to include interactive elements such as embedded code, multimedia (e.g., images, movies, 3D volumes), and datasets in their manuscripts. While advanced technical expertise is not required, familiarity with these tools will help you fully leverage the platform's capabilities. For new users, EM provides templates, documentation, and examples to guide you through the process. Please contact [Colin](mailto:cophus@stanford.edu) or [George](mailto:gvarnavides@berkeley.edu) if you need some help getting started! +The EM platform uses open-source technologies such as [MyST Markdown](https://mystmd.org/), [Jupyter Notebooks](https://jupyter.org/), and [conda](https://docs.conda.io/projects/conda/en/latest/index.html#)/[uv](https://docs.astral.sh/uv/) for environment management. +Authors are encouraged to include interactive elements such as embedded code, multimedia (e.g., images, movies, 3D volumes), and datasets in their manuscripts. +While advanced technical expertise is not required, familiarity with these tools will help you fully leverage the platform's capabilities. +For new users, EM provides templates, documentation, and examples to guide you through the process. +Please contact [Colin](mailto:cophus@stanford.edu) or [George](mailto:gvarnavides@berkeley.edu) if you need some help getting started! --- @@ -20,14 +26,14 @@ The EM platform uses open-source technologies such as MyST Markdown, Jupyter Not ### Step 1: Setting Up Your Environment 1. **Clone the Repository** - - Fork the [EM Quickstart](https://github.com/msa-em/em-quickstart), [EM Template](https://github.com/msa-em/em-template), or another EM article from [GitHub](https://github.com/msa-em). + - Fork the [EM Quickstart](https://github.com/msa-em/em-quickstart), [EM Template](https://github.com/msa-em/em-template), or another EM article from [GitHub](https://github.com/msa-em) and give it a descriptive name. - Clone your fork: ``` - git clone git@github.com:msa-em/.git + git clone git@github.com:/.git ``` - Switch to the `dev` branch: ``` - git checkout dev + git checkout -b dev ``` 2. **Configure the Environment** @@ -47,6 +53,9 @@ The EM platform uses open-source technologies such as MyST Markdown, Jupyter Not conda activate ``` +```{note} +If you are familiar with the next generation package manager, [uv](https://docs.astral.sh/uv/), you can instead clone the [EM Quickstart uv](https://github.com/msa-em/em-quickstart-uv) repository and follow the instructions there. +``` ### Step 2: Editing Your Article @@ -72,19 +81,21 @@ The EM platform uses open-source technologies such as MyST Markdown, Jupyter Not ``` **Add Your Article Content** - - Write your manuscript in MyST Markdown, making sure to organize your sections into separate markdown files, and using subsections where appropriate. As you write the article content, embed code, multimedia, and data as needed. + - Write your manuscript in MyST Markdown, making sure to organize your sections into separate markdown files, and using subsections where appropriate. + As you write the article content, embed code, multimedia, and data as needed. - Remember that when committing your local `myst.yml` changes, you will need to switch back to `jupyter: true` for the web-based version. - ### Step 3: Previewing and Finalizing **Preview Your Article** - Push your changes to the `dev` branch. - - Open a draft pull request (PR) into the `main` branch. GitHub Actions will deploy a staging site for live previews. + - Open a draft pull request (PR) into the `main` branch. + GitHub Actions will deploy a staging site for live previews. - Click the "Inspect" link in the GitHub Actions bot message to preview your article on the Curvenote staging site. **Merge When Ready** - - Once all content is finalized, merge the PR into the `main` branch. Ensure thematic changes are grouped together. + - Once all content is finalized, merge the PR into the `main` branch. + Ensure thematic changes are grouped together. --- @@ -93,14 +104,15 @@ The EM platform uses open-source technologies such as MyST Markdown, Jupyter Not ### Getting Started -If you're new to the tools and processes used for Elemental Microscopy, follow these simpler steps to get started without using GitHub or advanced command-line tools. These instructions will guide you through preparing and submitting your manuscript. +If you're new to the tools and processes used for Elemental Microscopy, follow these simpler steps to get started without using GitHub or advanced command-line tools. +These instructions will guide you through preparing and submitting your manuscript. ### Step 1: Download Template - Choose a template to get started, either: - - The [EM Quickstart Template](https://github.com/msa-em/em-quickstart). - - The [full EM Template](https://github.com/msa-em/em-template). + - The [EM Quickstart Template](https://github.com/msa-em/em-quickstart). + - The [full EM Template](https://github.com/msa-em/em-template). - The templates includes basic formatting, example figures, and placeholders for multimedia or code. - - Save the template to your computer and open it using any Markdown-compatible editor (e.g., [Sublime](https://www.sublimetext.com/),, [Typora](https://typora.io/), [Visual Studio Code](https://code.visualstudio.com/), or a simple text editor). + - Save the template to your computer and open it using any Markdown-compatible editor (e.g., [Sublime](https://www.sublimetext.com/), [Typora](https://typora.io/), [Visual Studio Code](https://code.visualstudio.com/), or a simple text editor). ### Step 2: Edit Your Manuscript - Use the downloaded template to write your article, ensuring you: @@ -109,7 +121,8 @@ If you're new to the tools and processes used for Elemental Microscopy, follow t - Include inline code examples or results, if applicable. ### Step 3: Interactive Content - - If you want to include interactive visualizations or code, let the editorial team know. They will guide you on how to use pre-configured Jupyter notebooks or help integrate the interactive elements for you. + - If you want to include interactive visualizations or code, let the editorial team know. + They will guide you on how to use pre-configured Jupyter notebooks or help integrate the interactive elements with you. ### Step 4: Preview Article - After editing, send your manuscript and associated files (e.g., images, datasets) to the editorial team, either [Colin](mailto:cophus@stanford.edu) or [George](mailto:gvarnavides@berkeley.edu). @@ -122,13 +135,13 @@ If you're new to the tools and processes used for Elemental Microscopy, follow t ### Notes for Beginner Authors -- **No Installation Required**: Beginner authors do not need to set up a local environment or use GitHub. All technical configurations will be handled by the editorial team. -- **Focus on Content**: Concentrate on the clarity and organization of your article. The editorial team will assist with integrating multimedia and code. - +- **No Installation Required**: Beginner authors do not need to set up a local environment or use GitHub. +All technical configurations will be handled by the editorial team. +- **Focus on Content**: Concentrate on the clarity and organization of your article. +The editorial team will assist with integrating multimedia and code. --- - ## Best Practices - Use templates and examples provided in the repository to guide your writing. @@ -136,4 +149,3 @@ If you're new to the tools and processes used for Elemental Microscopy, follow t - Cite datasets and code repositories using DOIs where possible. For further assistance, please contact the editorial team at [elementalmicroscopy.com](/editors). - From d3a433960a005c86b2d96b2c7c001dca9f66726f Mon Sep 17 00:00:00 2001 From: gvarnavi Date: Sat, 25 Jan 2025 17:07:17 -0800 Subject: [PATCH 05/10] editorial team changes --- editors.md | 29 ++++++++++++++++++++++------- 1 file changed, 22 insertions(+), 7 deletions(-) diff --git a/editors.md b/editors.md index c8e2675..1b90331 100644 --- a/editors.md +++ b/editors.md @@ -1,23 +1,37 @@ --- title: Editors and Developers -description: Elemental Microscopy is headed up by Editor-in-Chief, Colin Ophus and is part of the Microscopy Society of America. +description: Elemental Microscopy is headed by Editor-in-Chief, Colin Ophus, Technology Editor, Georgios Varnavides, and is part of the Microscopy Society of America. --- ## Editors -`Colin Ophus` is an [Associate Professor](https://colab.stanford.edu/people) in the [Department of Materials Science and Engineering](https://mse.stanford.edu/) at [Stanford University](https://www.stanford.edu/), and a Center Fellow at the [Precourt Institute for Energy](https://energy.stanford.edu/). He was formerly a staff scientist at the [National Center for Electron Microscopy](https://foundry.lbl.gov/about/facilities/the-national-center-for-electron-microscopy-ncem/), part of the [Molecular Foundry](https://foundry.lbl.gov/), at [Lawrence Berkeley National Lab](https://www.lbl.gov/). He researchs experimental methods, reconstruction algorithms, and data analysis for TEM. He has received a US DOE Early Career award (2018) and was awarded the [Burton Medal](https://www.microscopy.org/awards/bios/burton_physical_2022.cfm) from the Microscopy Society of America (2022). He is project leader for the [Prismatic](https://prism-em.com/) STEM simulation and [py4DSTEM](https://github.com/py4dstem/py4DSTEM) open-source codes. He is the founding editor-in-chief for `Elemental Microscopy`. (cophus@stanford.edu) +`Colin Ophus` is an [Associate Professor](https://colab.stanford.edu/people) in the [Department of Materials Science and Engineering](https://mse.stanford.edu/) at [Stanford University](https://www.stanford.edu/), and a Center Fellow at the [Precourt Institute for Energy](https://energy.stanford.edu/). +He was formerly a staff scientist at the [National Center for Electron Microscopy](https://foundry.lbl.gov/about/facilities/the-national-center-for-electron-microscopy-ncem/), part of the [Molecular Foundry](https://foundry.lbl.gov/), at [Lawrence Berkeley National Lab](https://www.lbl.gov/). +He researches experimental methods, reconstruction algorithms, and data analysis for S/TEM. +He has received a US DOE Early Career award (2018) and was awarded the [Burton Medal](https://www.microscopy.org/awards/bios/burton_physical_2022.cfm) from the Microscopy Society of America (2022). +He is project leader for the [Prismatic](https://prism-em.com/) STEM simulation and [py4DSTEM](https://github.com/py4dstem/py4DSTEM) open-source codes. +He is the founding editor-in-chief for `Elemental Microscopy`. +He can be reached at cophus@stanford.edu -`Georgios Varnavides` is a Miller Fellow postdoc working at the University of California, Berkeley and Lawrence Berkeley National Lab. He is the technology editor for `Elemental Microscopy`. (gvarnavides@berkeley.edu) +`Georgios Varnavides` is a [Miller Fellow](https://miller.berkeley.edu/) postdoctoral researcher working at the University of California, Berkeley and Lawrence Berkeley National Lab. +His research interests lie in developing new computational imaging modalities to observe the structure and function of materials at high resolution and sensitivity. +He is one of the core developers of the phase-retrieval modules in the [py4DSTEM](https://github.com/py4dstem/py4DSTEM) open-source code. +He is the technology editor for `Elemental Microscopy`, with extensive experience in using web-based open-source tools for pedagogy and science-communication. +He can be reached at gvarnavides@berkeley.edu. ## Editorial Board -`Beth Dickey` is the Department Head and Teddy and Wilton Hawkins Distinguished Professor of the [Materials Science and Engineering](https://www.mse.engineering.cmu.edu/index.html) department at [Carnegie Mellon](https://www.cmu.edu/). She is a Fellow of the Microscopy Society of America and of the American Ceramic Society, and is a member of the World Academy of Ceramics. (ecdickey@cmu.edu) +`Beth Dickey` is the Department Head and Teddy and Wilton Hawkins Distinguished Professor of the [Materials Science and Engineering](https://www.mse.engineering.cmu.edu/index.html) department at [Carnegie Mellon](https://www.cmu.edu/). +She is a Fellow of the Microscopy Society of America and of the American Ceramic Society, and is a member of the World Academy of Ceramics. (ecdickey@cmu.edu) -We are currently recruiting additional members of the editorial board! Contact [Colin Ophus](mailto:cophus@stanford.edu) if you are interested. +```{important} +We are currently recruiting additional members of the editorial board! +Contact [Colin Ophus](mailto:cophus@stanford.edu) if you are interested. +``` --- @@ -25,9 +39,10 @@ We are currently recruiting additional members of the editorial board! Contact [ The Elemental Microscopy journal was developed by the [Curvenote](https://curvenote.com/mission) team and built with open source [MyST Markdown](https://mystmd.org) components. -`Rowan Cockett` is the CEO and co-founder of [Curvenote](https://curvenote.com), which is an interactive, online writing and publishing platform for science, with dedicated integrations to Jupyter. Rowan is a core developer of [MyST Markdown](https://mystmd.org/) and has a Ph.D. in computational geophysics from the University of British Columbia (UBC) where he worked on large-scale simulation and parameter estimation package for geophysical processes (electromagnetics, fluid-flow, gravity, etc.). +`Rowan Cockett` is the CEO and co-founder of [Curvenote](https://curvenote.com), which is an interactive, online writing and publishing platform for science, with dedicated integrations to Jupyter. +Rowan is a core developer of [MyST Markdown](https://mystmd.org/) and has a Ph.D. in computational geophysics from the University of British Columbia (UBC) where he worked on large-scale simulation and parameter estimation package for geophysical processes (electromagnetics, fluid-flow, gravity, etc.). -The larger [Curvenote team](https://curvenote.com/mission) including `Steve Purves`, `Franklin Koch` and `Mike Morrison` have been in involved in the design and development of Elemental Microscopy. +The larger [Curvenote team](https://curvenote.com/mission) including `Steve Purves`, `Franklin Koch`, and `Mike Morrison` have been in involved in the design and development of Elemental Microscopy. --- From 7c53cb552706f68a99e8eeaab0dd4d8417dc1ba1 Mon Sep 17 00:00:00 2001 From: gvarnavi Date: Sat, 25 Jan 2025 17:08:23 -0800 Subject: [PATCH 06/10] added some more abbreviations --- myst.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/myst.yml b/myst.yml index 1cc7e29..151edfb 100644 --- a/myst.yml +++ b/myst.yml @@ -9,6 +9,8 @@ project: NCEM: National Center for Electron Microscopy TEM: transmission electron microscopy STEM: scanning transmission electron microscopy + S/TEM: scanning transmission electron microscopy + MSA: microscopy society of America US: United States site: title: Elemental Microscopy From 44b098a6666535efdc7618d09776ac58c170c1a1 Mon Sep 17 00:00:00 2001 From: gvarnavi Date: Sat, 25 Jan 2025 17:16:56 -0800 Subject: [PATCH 07/10] upgrading toc --- _toc.yml | 10 ---------- myst.yml | 8 ++++++++ 2 files changed, 8 insertions(+), 10 deletions(-) delete mode 100644 _toc.yml diff --git a/_toc.yml b/_toc.yml deleted file mode 100644 index 9f672b6..0000000 --- a/_toc.yml +++ /dev/null @@ -1,10 +0,0 @@ -# Table of contents -# Learn more at https://jupyterbook.org/customize/toc.html - -format: jb-book -root: index -chapters: - - file: overview - - file: articles - - file: writing-an-article - - file: editors diff --git a/myst.yml b/myst.yml index 151edfb..edcf391 100644 --- a/myst.yml +++ b/myst.yml @@ -12,6 +12,14 @@ project: S/TEM: scanning transmission electron microscopy MSA: microscopy society of America US: United States + toc: + # Auto-generated by `myst init --write-toc` + - file: index.md + - file: overview.md + - file: articles.md + - file: writing-an-article.md + - file: editors.md + site: title: Elemental Microscopy logo_text: EM From 9c274b8e823193e2f0bf9e97f30e3e949a1091f2 Mon Sep 17 00:00:00 2001 From: Georgios Varnavides Date: Sat, 25 Jan 2025 18:10:23 -0800 Subject: [PATCH 08/10] Create preview.yml --- .github/workflows/preview.yml | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 .github/workflows/preview.yml diff --git a/.github/workflows/preview.yml b/.github/workflows/preview.yml new file mode 100644 index 0000000..1c68782 --- /dev/null +++ b/.github/workflows/preview.yml @@ -0,0 +1,21 @@ +name: Curvenote Deploy Preview +on: + pull_request: + branches: ['main'] +permissions: + contents: read + pull-requests: write +concurrency: + group: 'preview-pages' + cancel-in-progress: false +jobs: + build-and-deploy-preview: + runs-on: ubuntu-latest + steps: + - name: Deploy Preview 🚀 + uses: curvenote/action-myst-publish@v1 + env: + CURVENOTE_TOKEN: ${{ secrets.CURVENOTE_TOKEN }} + with: + preview: true + preview_subdomain: microscopy_bot-myst_preview From c7f825c6900c7db3336785fd1b4350bd10f17669 Mon Sep 17 00:00:00 2001 From: Georgios Varnavides Date: Sat, 25 Jan 2025 18:34:30 -0800 Subject: [PATCH 09/10] Update preview.yml --- .github/workflows/preview.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/preview.yml b/.github/workflows/preview.yml index 1c68782..009fd7f 100644 --- a/.github/workflows/preview.yml +++ b/.github/workflows/preview.yml @@ -18,4 +18,4 @@ jobs: CURVENOTE_TOKEN: ${{ secrets.CURVENOTE_TOKEN }} with: preview: true - preview_subdomain: microscopy_bot-myst_preview + preview_subdomain: microscopy-myst_preview From 1d0f3263bbdad338e6d61ce1b31d9a4481d51905 Mon Sep 17 00:00:00 2001 From: cophus Date: Sun, 26 Jan 2025 18:01:15 -0800 Subject: [PATCH 10/10] Minor tweaks --- editors.md | 26 ++++++++++++++++---------- index.md | 2 +- myst.yml | 2 ++ overview.md | 12 +++++++----- writing-an-article.md | 4 ++-- 5 files changed, 28 insertions(+), 18 deletions(-) diff --git a/editors.md b/editors.md index 1b90331..6913e1e 100644 --- a/editors.md +++ b/editors.md @@ -5,34 +5,40 @@ description: Elemental Microscopy is headed by Editor-in-Chief, Colin Ophus, Tec ## Editors -`Colin Ophus` is an [Associate Professor](https://colab.stanford.edu/people) in the [Department of Materials Science and Engineering](https://mse.stanford.edu/) at [Stanford University](https://www.stanford.edu/), and a Center Fellow at the [Precourt Institute for Energy](https://energy.stanford.edu/). +`Colin Ophus` is an Associate Professor in the [Department of Materials Science and Engineering](https://mse.stanford.edu/) at [Stanford University](https://www.stanford.edu/), and a Center Fellow at the [Precourt Institute for Energy](https://energy.stanford.edu/). He was formerly a staff scientist at the [National Center for Electron Microscopy](https://foundry.lbl.gov/about/facilities/the-national-center-for-electron-microscopy-ncem/), part of the [Molecular Foundry](https://foundry.lbl.gov/), at [Lawrence Berkeley National Lab](https://www.lbl.gov/). He researches experimental methods, reconstruction algorithms, and data analysis for S/TEM. He has received a US DOE Early Career award (2018) and was awarded the [Burton Medal](https://www.microscopy.org/awards/bios/burton_physical_2022.cfm) from the Microscopy Society of America (2022). He is project leader for the [Prismatic](https://prism-em.com/) STEM simulation and [py4DSTEM](https://github.com/py4dstem/py4DSTEM) open-source codes. He is the founding editor-in-chief for `Elemental Microscopy`. -He can be reached at cophus@stanford.edu +[Email](mailto:cophus@stanford.edu) +[Website](https://colab.stanford.edu/people) + `Georgios Varnavides` is a [Miller Fellow](https://miller.berkeley.edu/) postdoctoral researcher working at the University of California, Berkeley and Lawrence Berkeley National Lab. His research interests lie in developing new computational imaging modalities to observe the structure and function of materials at high resolution and sensitivity. He is one of the core developers of the phase-retrieval modules in the [py4DSTEM](https://github.com/py4dstem/py4DSTEM) open-source code. He is the technology editor for `Elemental Microscopy`, with extensive experience in using web-based open-source tools for pedagogy and science-communication. -He can be reached at gvarnavides@berkeley.edu. - - -## Editorial Board +[Email](mailto:gvarnavides@berkeley.edu) +[Website](https://gvarnavides.com/) -`Beth Dickey` is the Department Head and Teddy and Wilton Hawkins Distinguished Professor of the [Materials Science and Engineering](https://www.mse.engineering.cmu.edu/index.html) department at [Carnegie Mellon](https://www.cmu.edu/). -She is a Fellow of the Microscopy Society of America and of the American Ceramic Society, and is a member of the World Academy of Ceramics. (ecdickey@cmu.edu) ```{important} -We are currently recruiting additional members of the editorial board! -Contact [Colin Ophus](mailto:cophus@stanford.edu) if you are interested. +We are currently recruiting additional editoris and members of the editorial board! +Contact [Colin](mailto:cophus@stanford.edu) if you are interested. ``` + +## Editorial Board + + +`Beth Dickey` is the Department Head and Teddy and Wilton Hawkins Distinguished Professor of the [Materials Science and Engineering](https://www.mse.engineering.cmu.edu/index.html) department at [Carnegie Mellon](https://www.cmu.edu/). +She is a Fellow of the Microscopy Society of America and of the American Ceramic Society, and is a member of the World Academy of Ceramics. +[Email](mailto:ecdickey@cmu.edu) + --- ## Technology diff --git a/index.md b/index.md index 3aee50d..40c65df 100644 --- a/index.md +++ b/index.md @@ -6,7 +6,7 @@ description: Elemental Microscopy is an online journal published by the Microsco `Elemental Microscopy` is an online journal published by the [Microscopy Society of America](https://www.microscopy.org/). Our articles are highly interactive, leveraging the power of open-source scientific programming communities, and modern internet technologies. -We offer reviews and tutorial treatments of key topics, ranging from fundamental theory, instrumentation advancements, experimental methods and data analysis. +We offer reviews and tutorial treatments of key topics in **microscopy**, ranging from fundamental theory, instrumentation advancements, experimental methods and data analysis. These articles offer cutting-edge insights into emerging applications in a variety of areas including **biology**, **life sciences**, **geology**, **engineering**, **materials science**, **nanoscience**, **physics**, and **archeology**. With embedded video, interactive code, and data content, the publications serve as excellent educational resources for the microscopy and the broader science community. Regularly updated and developed specifically for a digital environment, this journal is a dynamic and enduring reference resource for students, researchers, and practitioners in microscopy. diff --git a/myst.yml b/myst.yml index edcf391..11265d5 100644 --- a/myst.yml +++ b/myst.yml @@ -3,8 +3,10 @@ project: title: Elemental Microscopy open_access: true abbreviations: + APC: article processing charge CC BY 4.0: Creative Commons Attribution 4.0 International DOE: Department of Energy + DOI: digital object identifier MyST: Markedly Structured Text NCEM: National Center for Electron Microscopy TEM: transmission electron microscopy diff --git a/overview.md b/overview.md index 38e73a3..dd2b979 100644 --- a/overview.md +++ b/overview.md @@ -6,9 +6,11 @@ description: Publishing in Elemental Microscopy allows you to publish experiment ## Overview -Publishing in **Elemental Microscopy (EM)** provides a groundbreaking way to share experimental data through **highly interactive figures** and **dynamic content**. +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 @@ -17,9 +19,9 @@ One of the most significant advantages of publishing in `Elemental Microscopy` i - **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. +- **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. @@ -27,7 +29,7 @@ Interactivity can make your research more engaging and enable readers to explore ## Code -`Elemental Microscopy` is built on the **Jupyter Book publishing platform** and **MyST Markdown**, allowing seamless integration of **Jupyter notebooks**. +`Elemental Microscopy` is built on the [**Jupyter Book**](https://jupyterbook.org/en/stable/intro.html) publishing platform and [**MyST Markdown**](https://mystmd.org/) typesetting language, allowing seamless integration of [**Jupyter notebooks**](https://jupyter.org/). Authors can: - Reproduce workflows for visualization, analysis, and simulation directly in the article. diff --git a/writing-an-article.md b/writing-an-article.md index d0d21f4..719528d 100644 --- a/writing-an-article.md +++ b/writing-an-article.md @@ -6,8 +6,8 @@ short_title: '' ```{important} -The submission process is currently invite only! -Please get in touch with [Colin](mailto:cophus@stanford.edu) or [George](mailto:gvarnavides@berkeley.edu) if you are interested in writing an article for `Elemental Microscopy`. +The submission process currently requires communicating with an `EM` editor. +Please get in touch with [Colin](mailto:cophus@stanford.edu) or [George](mailto:gvarnavides@berkeley.edu) if you are interested in submitting an article for `Elemental Microscopy`. ``` These instructions will help you prepare and submit your manuscript using the EM platform.