Graphics Exercise – making publication quality scientific graphics

OK – you’re at university doing a chemistry degree (although this exercise is also relevant to pretty much any science degree)– so why should you be learning graphic design skills?

While you are at university, you will need to create your own graphics, diagrams and figures for lab reports, posters, presentations and project reports. Getting good at making figures will save you time and get you higher marks.

Even more importantly, at some point you intend to graduate!  Some of you may end up going into science related jobs where you will need to make figures, diagrams and graphics for journal articles, posters and presentations, and scientific reports.

A significant number of you will go into non-science related fields – but you will probably also need to make your own graphics too. And, even if you are working as scientist, you will also need to produce figures for other purposes.  For example, in my career, I have had to make plans for new laboratories and equipment; design new logos for events and teams; make maps and signs for meetings; design business cards; and many other tasks that have required that I can make good quality graphics.

In the modern workplace, knowing how to make good graphics is a very valuable transferable skill.

In this exercise, we will use free software to make a publication quality, scientific figure – a bit like this one:

The aim of the exercise is to give you experience of using several programs that specialise in different areas of graphics design and production.  We are using these programs in one way here, but hopefully you will see other ways you could use the same tools for other graphics tasks.  I can’t stress enough that you will benefit even more from playing around with these tools and finding out what else you can do with them.

Bitmap vs Vector Graphics

The most common graphics formats generally are of a type known as bitmap or raster graphics.  This is the kind of file that is used to store photographs electronically – like jpegs or pngs.  But, for scientific figures,  diagrams and logos, a different file format tends to be used – vector format.

Bitmap graphics take the illustration and divide it into tiny squares (known as pixels – picture elements).  Each pixel is given a colour and brightness value. This style of image is great for photos.  But, it has a weakness.  Once the image file is created, the number of pixels is fixed.  So, what happens when or if you want to make the image bigger?  You can’t create any more pixels, so the image tends to end up look blurry or pixelated.

In vector graphics, the illustration is not saved pixel by pixel.  Instead, all the parts of the image are defined by the coordinates of the lines and corners that make up the image, and of the colours of the shapes inside those lines.  Then, no matter how you scale the image, the illustration can be recreated perfectly, without any pixelation. That is why scientific diagrams, figures and illustrations are often made as vector images instead of bitmap graphics.

You can find out more from these links:

In this exercise  we will use a variety of formats, some bitmap and some vector.

Bitmap formats we will use:

  • jpg/jpeg
  • png
  • tiff/tif

Vector formats we will use:

  • svg
  • pdf
  • eps
  • emf/wmf

Note – remember that vector format files can contain bitmap images as part of the vector format image.  The vector parts will scale well, but the bitmap parts will be as susceptible to pixelation as straight bitmap images themselves.

Getting the Software

The three tools we will use are:

  • SciDAVIS
  • Inkscape
  • GIMP

These are all really high quality and can be used on different platforms.  Even better – they are free.  Why is this important?  We could teach you how to use expensive commercial software but when you leave university, not everyone has access to these programs.  You can always get hold of these free alternatives, however.  So, the skills you learn with these tools will be portable to wherever you go next.

We have made the programs available on our university computers (through the “software hub”).  But you can also get them for your own computers and do the exercise on them.

SciDAVis

SciDAVis is a fantastic free application for Scientific Data Analysis and Visualization. It is mainly designed for plotting and fitting scientific data.  Unlike the most common commercial tool, Origin, SciDAVis is free, so students can install it on their own laptops and use it to process their own lab and project data.

You can find out more about SciDAVis here:

You can also find useful tutorial videos on the internet to help you learn how to use it.  For example:

(At least watch the first one before the Graphics Workshop)

Inkscape

Inkscape is a fabulous vector drawing program that is both free and open source. It is as powerful as expensive, commercial software and will probably provide all the capability you will ever need.  A commercial alternative is Abode Illustrator.  I use Inkscape as my main tool for producing schematics, labeling figures, scaling graphics and graphs and for designing rapid prototyping parts.

You can find out more information about Inkscape here:

As with SciDAVIs, there are many useful tutorial videos online:

(At least watch the first one before the Graphics Workshop)

https://youtu.be/XuMGaZKjX1A

GIMP

GIMP stands for the GNU Image Manipulation Program. It is free and open source software for image editing and creation – providing a lot of the same functionality as Photoshop or other similar programs.

You can find more about GIMP here:

As with the other programs we will use, there are lots of great online tutorial videos to help you undertake tasks with GIMP:

(At least watch the first one before the Graphics Workshop)

Journal Requirements

Scientific journals often have very specific requirements for the figures that you wish to include in papers.  If your figures don’t meet those requirements then your paper will probably simply be rejected.  so, it is important that you read and can understand all the different requirements.  As an added complication, not all journals have the same requirements!

Look at the similarities and differences between the requirements of these two journals:

And, note that these are both Wiley journals.

There may be other requirements for figures destined for other purposes – e.g. posters, presentations, reports etc.

General figure making hints

In general though there are some common core features when making graphics:

  • Make your figures at the size they should be in the final paper/report/poster or whatever.
  • Make the final versions of photographs or similar figures as bitmap formats (tiff being the most widely accepted) – and with resolutions of 300 or even better 600 dpi.
  • Make the final versions of schematics; chemical structures or schemes; diagrams; graphs or spectra; etc as vector format graphics (eps, emf/wmf and pdf being the most commonly used formats)

So, in this exercise, you will learn how to:

  • Make high quality graphics using multiple programs
  • Scale graphics to specific sizes
  • Convert diagrams and figures to specific bitmap file formats (png, jpeg and tiff) at the appropriate resolutions
  • Export vector graphics as eps, emf/wmf and pdf filetypes – and see when each should be used

The Exercise

So, we’ve looked at the background to the task.  We’ve looked at the differences between bitmap and vector graphics and at the different software packages that we are going to use to create a figure that looks like this:

Each one of the different software tools we are using is there to do a specific job:

(Watch this video before the workshop)

We will use:

  • SciDAVis
    • import the spectrum data from a csv file
    • plot the spectrum data and
    • export the resulting basic figure as a vector format svg file.
  • Inkscape
    • import the svg format file from SciDAVis
    • add and position the annotations
    • rescale the figure to specific sizes
    • save the completed figure as an svg file
    • export the figure as different vector file formats – eps, emf and pdf
    • export the image as a bitmap file (png format) with specific resolution
  • GIMP
    • convert the png file saved from Inkscape into jpeg and tiff formats

You can get the data that is needed for the exercise (in a csv file) from here.

Watch all of the following videos before the workshop – or you will be very pressed for time!

Exercise – Making the Figure step 1 – SciDAVIS

Note – You can see the video in full screen – click the little square button on the bottom right of the YouTube frame.  You can also force YouTube to show you the video in high resolution (if it is not doing so already) using the little gear wheel icon at the bottom of the YouTube screen above.

Making the Figure step 2 – Editing and annotating in Inkscape

Making the Figure step 3 – Exporting figures in different formats

Submitting the figures

If you are doing this class as one of my modules, then you should be submitting all the different figure formats you have created and the PowerPoint file that was described in the video.  You will be given a submission link for this. (If I haven’t given you one  – ask!)