Inkscape Scientific Figure Template

A simple Inkscape template for scientific figures 🎨

Contains sets of colors, text, and annotations to have a solid starting point for figure creation.

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Notes and other useful things

• Colororacle to check visibility with vision impairments.
• The Paul Tol colors are used by the SciencePlots package.
• Plugins: TexText, Scientific Inkscape, inkscapeMadeEasy, ProPlot, ...

Fiji: Images to svg vector graphics

• Export via Biovoxxel Figure Tools
• Open the svg image in Inkscape
• Fiji annotations (e.g., scale bars from em-scalebartools) must be unlocked (Object -> Unlock All) and then ungrouped (Shift+Ctrl+G) for editing

Inkscape batch export to different formats

Figures may be needed in different file formats:

• An inital manuscript draft in Word may have smaller rasterized images (e.g., 300 dpi png) to reduce file size.
• A journal may require a specific file format during submission.

It can be tedious to manually export all figures to these formats. One can use the Inkscape command line to help with this issue. It can be used to batch export all svgs in a folder to the desired format!

• Prepare your Inkscape figure, set the figure area as the 'Page' in Inkscape by selecting the relevant figure area and using Shift+Ctrl+R ('Resize Page to Selection')
• I recommend putting a copy of each finalized figure in a separate folder, so that one has only the up-to-date svgs in it: Figure-1.svg, Figure-2.svg, ...
• Start a terminal/Windows command line (type cmd in the address bar in Windows) in this folder and run the desired export command.

Examples: Batch export on Windows to 600 dpi (control via -d 600) PNGs. Run the following command from a folder containing the Inkscape SVGs:

  for %f in (*.svg) do "C:\Program Files\Inkscape\bin\inkscape.com" --export-filename=%~nf.png -d 600 %~nf.svg

Export on Windows to PDF:

for %f in (*.svg) do "C:\Program Files\Inkscape\bin\inkscape.com" --export-filename=%~nf.pdf %~nf.svg

Export on Windows to EPS:

for %f in (*.svg) do "C:\Program Files\Inkscape\bin\inkscape.com" --export-filename=%~nf.eps %~nf.svg

File compression

• OptiPNG - Lossless PNG file compression. Especially useful if you want to maximize quality of a PNG in an upload mask with a file-size limit (e.g., 500 kB for an abstract submission).
  Batch conversion of all PNGs in a folder on Windows (copy the optipng.exe to the same folder):

    for %f in (*.png) do optipng.exe %f

Paper

• Jambor et al., Creating Clear and Informative Image-Based Figures for Scientific Publications PLOS Biology 2021, 19 (3), e3001161. https://doi.org/10.1371/journal.pbio.3001161.
• Crameri, Shephard and Heron The Misuse of Colour in Science Communication Nat Commun 2020, 11 (1), 5444. https://doi.org/10.1038/s41467-020-19160-7.
• Schmied et al. Community-Developed Checklists for Publishing Images and Image Analysis arXiv February 14, 2023. https://doi.org/10.48550/arXiv.2302.07005.