Introduction to course

Introduction to course#

This course shows in practice how to create an image figure for publication using Fiji and Inkscape. The intention is to take one example from the original image and create a complete image figure, including the figure legend and methods used to create and process the images.

The result should be an image figure that truthfully and effectively reports the scientific result that the figure represents:

In

Fig. 9 Example of an image figure with key annotations provided, such as a scale bar and content including the shown image colors. An enlarged crop is shown next to the overview to focus the viewer on a key result. The origin of the crop is annotated in the overview. Additional annotations, such as white arrowheads, are used to further guide the viewer.#

Materials#

For this tutorial you are going to need:

The course shown here contains all necessary image data as a download. Alternatively, the input, processed, and result images can also be downloaded from a Zenodo repository.

Note

We selected these tools because they are free, open source, and familiar to the authors. The underlying principles, however, can be applied to other tools.

Checklist#

To help guide authors to create good image figures we have created a set of Checklists. This tutorial is based on a condensed version of the checklist (see Condensed checklists.).

In

Fig. 10 Condensed checklists.#

Table of contents#

  1. Unit 1: Visibility

  2. Unit 2: Format and annotations

  3. Unit 3: Figure and availability

  4. Unit 4: Quantification

  5. Background information

Further material#

Cheatsheets for creating image figures:

Schmied C. and Jambor HK. Effective image visualization for publications – a workflow using open access tools and concepts [version 2]. F1000Research 2021, 9:1373 (doi: 10.12688/f1000research.27140.2)

Images for the examples were published here:

Wolff C. et al. Morphological profiling data resource enables prediction of chemical compound properties. iScience 2025 (doi: 10.1016/j.isci.2025.112445)

Help#

If you need help write to the team on image.sc: https://forum.image.sc/tag/quarep.

You can also reach out to the creator of this tutorial: schmiedc