You’ve been diligently working on your current project for months and are finally at the point of presentation or publication. Fantastic! However, how you communicate your information is equally important to what you communicate. If information is not presented in an effective manner, your “take home message” and its impact are reduced; or even worse, information could be viewed as confusing or misleading.
There are a number of commercially available and open-source solutions for generating scientific figures, so that you can spend less time illustrating your data and more time actually communicating the data. For detailed diagrams, these tools can be invaluable, such as Biorender, which can truly streamline generating cell cycle figures; localization figures; and other similar highly details depictions of your data. But what if you need to generate some figures yourself; where would you begin? What software would you use?
Figures generated for both manuscripts as well as posters should ideally be designed in a vector based format so that they can be scaled virtually infinitely, ensuring legibility at all sizes, and avoiding pixelation which can occur with photos and non-vector illustrations. While a number of software solutions exist that enable the creation (or conversion) of images in a vector based format, Adobe Illustrator is one of the most popular, and will be the focus of this article. The advise provided below has been adapted from the YouTube video tutorial series published by the Stowers Institute for Medical Research. Below you will find a series of seven (7) YouTube tutorials that gradually progress through various aspects of figure creation using Illustrator. As a UCSC Graduate Student or Postdoc, you receive free access to Adobe Creative Cloud through your UCSC login, enabling you to download and use Adobe Illustrator for free to aid you in your figure creation.
Ethics and Contrast Adjustment
- It cannot be overstated how import accurate intensity representation in scientific images can be.
- Appropriate contrast adjustments are critical to ensure the visual representation aligns with the scientific statements being made.
- Different contrast settings can convey different information. Thus it is crucial to select a setting that is coherent with the scientific message being conveyed.
- Maintaining a visible background noise in images is crucial to prevent misinterpretation or unintentional concealment of data.
Real-World Examples and Fraud Prevention
- Check out examples from Retraction Watch to see how inappropriate image adjustments or manipulations can lead to data misrepresentation and subsequently, paper retractions.
- It cannot be understated how important it is to save raw data, including metadata, as a preventive measure against accusations of data manipulation or fraud.
- The Stowers Institute’s initiative of an “Original Data Repository” is one example of maintaining transparency and integrity in data presentation.
Image Scaling and Resolution
- Different interpolation methods (i.e. bilinear; bicubic) can impact both image quality and authenticity.
- While scaling images is sometimes necessary, it’s vital to use appropriate methods (preferably bilinear interpolation) and disclose the methodology in the materials and methods section of publications.
- Adobe Illustrator is recommended for figure layout due to its default settings that do not inappropriately process images and its support for vector graphics, which maintain quality upon scaling.
Journal Requirements
- Be sure to adhere to specific journal requirements regarding figure preparation and layout. Journals have different requirements so be sure to confirm (i.e. Science, Nature, JCB).
- Pay attention to key parameters such as figure width; height; color format (RGB or CMYK); and resolution (PPI/DPI). A general requirement of 300 PPI for high-resolution images tends to be consistent across various journals.
Setting Up Adobe Illustrator
- Always ensure your Illustrator document is initially setup for based on the chosen journal’s requirements. It can be very problematic to change these later.
- Optimize your Illustrator workspace for scientific figure preparation by organizing and adding relevant tools and windows, including swatches, attributes, character styles, glyphs, align, and transform options for easy access.
- Save time in the future by saving your customized workspace as a new preset (i.e. “Figure Prep”) and help to ensure consistency and ease of access to required tools during future use.
Record Keeping and Ethical Considerations
- Keep meticulous records to trace the origin of data used in figures, so that you can ensure accountability and the ability to validate and reproduce data upon request.
- It is your ethical obligation to accurately represent data, document any image edits, and ensure that such information is communicated transparently in any and all figure legends.
- Whenever possible, data should be made publicly available in its original format to ensure transparency and accessibility in scientific communication.
Managing Channels and Adjusting Brightness/Contrast
- When adjusting images, pay attention to the different image channels so that any adjustments to brightness and contrast ensure accurate representation while maintaining ethical considerations.
- Avoid over-adjustment that obscures background noise, while ensuring data is not unintentionally concealed or misrepresented.
Cropping and Duplicating Image Data
- Illustrator has a number of useful tools to aid with selecting a region of interest within an image, cropping, and duplicating it to create a focused image for figure preparation.
- Be sure to utilize and maintain consistent image sizes and shapes when presenting multiple images in a single figure panel to avoid miscommunication.
Ensuring Consistency Across Multiple Images
- Illustrator can easily “copy and paste” adjustments, enabling easy propagation of brightness/contrast adjustments across multiple similar images to ensure visual consistency in the final figure.
- The open-source tool Fiji features a “propagate” function within the brightness and contrast tool which allows users to apply identical adjustments to all open three-channel images, ensuring that they are presented with consistent visual parameters in the final figure.
Creating Composite Images and Adding Scale Bars
- When creating composite images, be sure to maintain identical color formats (i.e. RGB) and add scale bars to microscopy images to avoid in visual comparison.
- Fiji has very similar tools, allowing for easy addition of a scale bar, ensuring that the scale is accurately represented in the final figure in Illustrator.
Raster vs. Vector Graphics
- Pixelation can significantly detract from your message, thus understanding the distinction between raster graphics (a grid of pixels, each with an identity) and vector graphics (mathematically defined shapes and lines) is very useful.
- Microscopy data and images are raster graphics, but Illustrator is a vector graphics program, meaning images maintain their resolution when resized until they are rasterized.
Resizing and Positioning Images
- Illustrator allows for quick and easy resizing of images to ensure they are presented at an appropriate scale within the final figure.
- The SHIFT key can be invaluable in helping to maintain the aspect ratio of images while resizing; helping to ensure image integrity.
Utilizing Rulers and Guides
- Rulers and guides can be added to the Illustrator workspace to assist in positioning images accurately within document.
- Guides can be locked after creation, ensuring consistent positioning of images and elements within the figure.
Aligning and Distributing Images
- Illustrator features several easy to use alignment tools, allowing you to align images relative to a key object and distribute them evenly within the workspace.
- Consistent spacing between images is critical to ensuring a coherent and visually pleasing final figure layout.
Journal Requirements for Text
- Journals have various standard for text, including preferred fonts; permissible font sizes; and specifications for panel letters (i.e. Arial, 5-7 points for text, 8-point bold lowercase for panel letters in Nature).
Setting Up Text in Adobe Illustrator
- Illustrator has a myriad of options to adjust text to ensure it adheres to journal requirements and is visually coherent within the figure.
Utilizing Character Styles and Libraries
- Character styles and libraries are tools in Illustrator used to manage and consistently apply text attributes across figures.
- Creating character styles for different text elements (i.e. panel letters; labels) and saving them in a library can easily help ensure consistency and ease of text management across figures.
Aligning and Managing Text
- Text can be aligned relative to images and other text, ensuring it is positioned accurately and aesthetically within the figure.
- Effective creation and management of text for labels and scale bars is crucial to ensuring they are clear, accurate, and adhere to character styles defined within Illustrator.
Importing Graphs from Excel
- Graphs can be exported from Excel as PDFs, which as a vector graphics format are more reliably managed within Illustrator compared to direct copying and pasting.
- Once imported into Illustrator, imported graphs appear similar to their Excel versions but are composed of various vector drawing elements that can be manipulated within Illustrator.
Managing Layers and Clipping Groups
- The Layers tool in Illustrator is very useful in organizing and managing figures, particularly the various elements within an imported graph.
- You can remove clipping groups which can complicate editing by selecting all elements and using keyboard shortcuts to release clipping masks without altering the visual data.
Editing and Grouping Text and Elements
- When editing, grouping, and managing text within imported graphs, ensure they adhere to journal requirements and are visually coherent within the figure.
- Similar to text, Illustrator facilitates the creation, positioning, and resizing of graph elements, ensuring they adheres to predefined character styles and are accurately positioned relative to other elements within the figure.
Managing Line Weights and Colors
- Line weights (particularly within graphs) may have journal specific guidelines that can be easily adhered to while making them visually pleasing within the figure.
- Stroke weights of various lines within graphs can be individually selected and adjusted, ensuring they are neither too bold nor too faint, providing a clear and aesthetically pleasing visual representation of the data.
Managing Libraries and Swatches
- Adobe’s color tools assist in managing different color schemes through libraries and swatches, ensuring consistent and appealing color palettes across figures.
- The Adobe color tool allows users to explore various color combinations created by designers, which can be added to Illustrator libraries and utilized in figures.
Extracting Color Palettes
- Color palettes can be quickly extracted from existing images using Adobe’s color extraction tool, ensuring that preferred color schemes can be replicated and utilized.
- Images can be dragged and dropped into the tool, automatically extracting a color palette that can be saved to Illustrator libraries and applied to figures.
Recoloring Figures
- Recolor figures to ensure color palettes are applied consistently across various elements within the figure.
- Techniques such as “select same fill color” and “select same stroke color” can be utilized to ensure that all relevant elements are recolored simultaneously, maintaining visual coherence.
Accessibility and Color Blindness
- When selecting color palettes, be sure to ensure colors used are accessible to individuals with color blindness.
- Illustrator’s colorblind view options (i.e. protanopia) allows a preview of how figures appear to individuals with different types of color blindness, ensuring that visual data remains distinguishable.
- Design color palettes that are accessible, utilizing transitions between blue/magenta and green/orange/yellow, and varying darkness/lightness to enhance distinguishability.