How to create simple diagrams in Inkscape – a guide for scientists

Part of a scientific diagram created in inkscape showing plants

Over the last week I had some fun making a couple of diagrams for our World Congress of Soil Science 2022 poster. Not going to lie, it took me a while to put them together but I’m glad I took on the learning curve. I decided to use Inkscape create my images. I thought it might be useful if shared some of the things I learnt on how to create a diagram in Inkscape, so if you fancied using Inkscape too, you’ve got somewhere to start from. I’m definitely not an expert, not by any stretch of the imagination, but from one novice to another this is how I approached it.

This is for you if you need more than the free version of BioRender, which is amazing but is limited in output quality (dpi) and with what you can do in the images. There isn’t that many options in BioRender for plants and roots. By doing it myself I found some cool techniques that really look great for plants and roots.

Inkscape overview

Inkscape is a completely free graphics program in a similar league of the paid for alternative Adobe Illustrator. Don’t let the ‘free’ bit give you an indication that it’s any less capable. It is an incredibly powerful graphics editor, most of which is well beyond my understanding. Inkscape will probably do everything I (and you) will need to do for the purposes of research illustration. If occasional dabbling is what you’re after, and an upgrade from Paint, then Inkscape is perfect.

It works by using SVG files – also known as scalable vector graphs – which are a much better way to create images than a JPG or PNG for example. It means that you can scale up and down as needed without a loss of quality. Essential for producing large graphics for A0 size posters.

Equipment I used

I must make a disclaimer before I start though; I do have a graphics pad (-> H950P by Huion). I did find this super useful for creating the plant leaves. This is due to the fact it can detect pen pressure so it works well with the ‘Min’ and ‘Max’ functions of the pencil tool. A normal mouse isn’t pressure-sensitive so having a graphics pad was essential to get the leaf tapered blade effects. There’s probably ways round this but if you’re super keen, then it might be a sensible investment. Other than this though, I didn’t really feel the need to have one – the mouse and keyboard did the job just fine. And I would recommend an actual mouse over a touch-pad. I would have torn my hair out with a touch pad.

(Though I’ve just had a thought – could you use a stylus and a touch pad as an alternative of a graphics pad?! I don’t know the answer to that question…)

I managed to create my Inkscape diagram on a standard issue university laptop. The laptop did however start struggling a bit towards the end. Nothing major, but enough to not want to create something too much bigger.

Getting started to create a diagram in Inkscape

There are a million and one Inkscape tutorials on the web. I personally started with its inbuilt ones. They were enough to get me going with the basics. I only really did the first three, then skimmed through the rest. It probably took me an hour or two to work properly through these.

A screenshot of how to find the tutorials menu in Inkscape.
To find the tutorials menu in Inkscape, go to Help -> Tutorials -> start with Basic and then work your way down the list.

These got me understanding the basic aspects of Inkscape functionality and navigation. So start there and then the rest of this blog will make more sense. I’m not going to re-invent the wheel and write the basics here. Below I’ve highlighted some particularly useful things I learnt and/or are worth highlighting specifically.

But first, draw it out on paper

Before you go anywhere near creating your diagram in Inkscape, draw your image out on paper. What do you want to show? What do you want to include or exclude? What about the dimensions? I drew out several versions to make sure that everything fit together.

A sketch of my drawing in my dotted notebook. It may be rough but it helped me layout what I wanted to include.
I did some sketching in my notebook before I started to create my diagram in Inkscape

Setting image size in Inkscape

This took me a while to work out… With your above sketch in tow, work out the image dimensions and set them in File -> Document Properties. You’re welcome. Save and remember to save regularly. It’s too easy to get used to programs which make a lot of effort not to lose your work and/or are stored on the cloud. However Inkscape has none of the back-up functionality of Microsoft Office for example, so save it regularly.


The tutorials didn’t cover layers which came as a surprise. These were something I learnt about back when photography editing was something I dabbled in. Whilst not essential to using Inkscape, they improve its functionality massively. In fact to create a diagram with any software, they are essential. With layers, it’s as it sounds. You use different layers in your image, and the final image is a blend of all these together. So for example, my image had 7 layers, one for each major component. I actually started with another layer, which was a sketch layer to outline what I wanted where, making sure my pencil and paper sketch looked OK digitally.
With the snip below, you might be able to see why layers are useful. The ‘eye’ icon, means you can hide the layer so you can’t see it. Useful if you don’t want distractions or if you want to check what’s in a layer. The lock function is incredibly useful as this ensures that you can prevent any changes to another part of your image whilst working on another. Working on one layer, is a one stop trip to frustration. It’s harder to select areas of an image and move them around, easier to accidently delete bits and harder to make later edits. So I recommend you get to know layers.

The layers menu in Inkscape which shows that the diagram I made was composed of 7 layers.
Here you’ll see the different layers of my image

Select all ‘like’ areas

Selecting like areas was covered in the tutorial, but one I found it super useful when creating the diagram. That’s the option Edit -> Select Same. It’s basically when you want to select all areas of a layer that have the same properties e.g. colours, outline (stroke) etc. I found this useful when I was trying to blend the leaves and flowers.

![[Pasted image 20220720055231.png]]

How to find selecting all similar fill colours and outlines (also known as strokes) in Inkscape
Finding all bits of a diagram which are the same colour is a useful tool

The ‘clip’ function

I found the ‘clip’ function useful. It meant that I could ‘zoom’ into a part of image, whilst still retaining all the paths, so I could edit them separately.

The clip option in the Inkscape menu. A useful tool to highlight areas of the scientific diagram you created. Options given for clip are set, set inverse and release.
The menu options for clipping an image

I couldn’t tell you the ins and outs of clips vs masks, but have a play and see what they can do for you. Inkspace doesn’t delete the original cropped part so if you decide at a later date that you want to zoom in a bit more then that can be changed.

A zoomed in section, showing a clip of the the root I drew for my diagram in Inkscape. Highlights the root-soil interface.
A clipped or zoomed in section of the image. All the original detail is retained should you change your mind later. (C) Annette Raffan

The image above also made use of the ‘snapping’ function whereby the dotted zoom lines are ‘snapped’ to the relevant corners ensuring everything is connected. Another thing I’ll mention about the ‘zoomed’ image above is the round-ended pointer. A while ago I watched a webinar run by Shiz Aoki (CEO and co-founder of BioRender) and she highlighted the difference between the use of a pointy arrow and a rounded arrow. A pointy arrow indicates directionality whereas a rounded arrow (or other non-triangular shape..) should be used to add information. It’s hard to get over the scientific ‘precision’ provided by a point, rather than the general ‘accuracy’ provided by a non-point, but hey it makes sense.

Getting to know the ‘Path’ functions

I haven’t yet cracked how paths can join together yet, but it’s something I need to spend some time on when I create more diagrams in Inkscape in the future. Take the core setup I was trying to draw below. The top worked out how I wanted it, but the base, I couldn’t get to join properly so I just had an outline. It’s perfectly possible, I just haven’t worked it out yet!

An example of a buried core setup and how I couldn't get the base to merge properly. The base shows a brown ovel but should be just outlined in brown.
How I used gradients plus an example of how I couldn’t get the base of the core to merge how I wanted. I’m still learning! (c) Annette Raffan

The most amazing function, mentioned in the tutorial was that of increasing the outset of a path using ‘ctrl + )’. This made for some super cool root-soil interface ‘impact zones’. I altered the opacity of the new object (and sent it to the background) and what you end up with is a perfectly proportional expansion of the original shape (i.e. the root). This was super cool and I was so happy with this amazing function!

A zoomed in image showing the use of the outset method with a dark coloured root and then an outset of light brown.
A close-up of the root-soil interface and where the dotted lines snap to one another. (c) Annette Raffan

Play about with gradients

I also loved trying out gradients. They give a much better impression of 3D than a flat colour. I used them in making the tubes above and for the ‘aggregates’ in the soil. I even created a gradient outline for the roots of the plants, to give an impression that the central root vascular bundle tends to be more dense than the outer cortex.. and that the impact of roots on soil is not constant across their length.
It didn’t quite work out how I wanted it to, but it was a cool effect to try. I think I would have been better using the outset function mentioned above. However this has so much potential!

Brown wiggly roots on a white background that I drew for my diagram in Inkscape. Highlights the use of a gradient outline.
Cool gradient effect applied to the roots I drew in Inkscape. (c) Annette Raffan

Final comments on using Inkscape to create a scientific diagram

I still don’t use them enough, but I did find learning the keyboard shortcuts for things was pretty helpful. Still, it’s all work in progress. There was stuff I learnt at the end which would have been useful to know earlier in the process. It’s all part of starting creating simple diagrams in Inkscape for your research. But ‘ah wisnae gaing back tae do it again’ at that point! There’s only so many hours in the day. I hope that you find this useful. Is there anything else I should have included here? What are your favourite functions of Inkscape? I’d love to know if you found any of these techniques useful to create your own diagram in Inkscape.

And final, final, here’s what I created:

A example diagram created using Inkscape with Annette Raffan watermark
One of the two diagrams I created in Inkscape for my poster

All drawings and text copyright of Annette Raffan – please do not reproduce without permission.

Coffee I’m drinkingHorsham Coffee RoasterPeru, Gregorio Esquen, Lot 1 – I also fixed my Moka pot with PTFE tape, so it works properly now!

Books I’m currently reading: Strong Female Lead: Lessons from Women in Power by Arwa Mahdawi and The Highly Sensitive Person by Elaine Aron

Previous post: Five Things I Wished I’d Known as a New PhD Student

Annette Raffan

Annette is a mum of one and a postgraduate researcher at the University of Aberdeen. She loves learning about new things and sharing them with the world, particularly knowledge management, plant and soil science, the world of research and things she has read along the way.

2 thoughts on “How to create simple diagrams in Inkscape – a guide for scientists

  1. Pingback: Nine Essential Apps and Websites for My PhD Workflow - Annette Raffan

Leave a Reply

Your email address will not be published. Required fields are marked *

Recent Posts