Biocurious is a weblog about biology, quantified.

How do you make and share scientific figures?

by Andre on 11 June 2007

One of the most important parts of scientific communication is making figures that convey your results clearly and compellingly. These days, that means using software to arrange plots and images from other programs, add labels, and often draw simple cartoons or schematics to illustrate the central ideas. There are several features that I consider important for this kind of graphics software. It must support a variety of file formats and be able to export publication quality images. It should have convenient alignment tools so that your images can be easily centered with respect to each other or arranged into arrays. Importantly, the drawing tools should be flexible, give a clean professional looking end product, and not be to difficult to learn. These are not very stringent requirements as far as graphics applications go.

Since most science is collaborative (it’s rare to see single author papers in most journals), it’s also useful for each person involved in the project to have access to the same software for making corrections or suggestions for improvement. So the ideal scientific graphics software will also be compatible with several platforms (at least Windows and Mac) and cheap (preferably free).

Unfortunately, because of its ubiquity, Powerpoint is often the default choice for making figures despite its failure to meet most of the requirements outlined above. This is not acceptable to me, even though I’ve been using it recently because it’s what some of my collaborators use (before submitting anything to a journal I will most likely redo these figures in another program after the final versions have been agreed upon).

I’ve tried Omnigraffle and found that it was pretty good, but as far as I know, it’s only available for Macs. I haven’t used Illustrator but I’ve heard good things. Is it worth the money? Will I be able to convince collaborators to use it despite the cost?

What else is out there? What do you use for making figures?



  1. PhilipJ    3841 days ago    #

    For diagramming, I also use Omnigraffle. The one feature that continually drives me insane is the lack of a proper arc implementation, but there are workarounds.

    I’ve thought (only briefly) about maybe using TeX for figures, but I think the time-required-to-gain-proficiency to amount-of-time-used ratio is very, very small.

    From anecdotal evidence I would say Illustrator is quite common, but given the cost, I’ve never really played with it much.


  2. DavidH    3841 days ago    #

    I’m a big fan of Inkscape for illustration. R for graphs and charts, LaTeX for trees and tiers. I’d really like to use Illustrator for academic work, and I am a pragmatist about these sorts of things, but I really feel that there’s something important and essential about using open source tools for scientific work when possible.


  3. kh    3841 days ago    #

    For drawing figures, adding text over images, etc., I’d also vote Inkscape (www.inkscape.org). Its free and open source, and runs on Windows, OSX and Linux.

    The feature-set is a little unbalanced in places – as it’s an open source project, contributors tend to focus on features that interest them – but all the basics are there, and I’ve successfully used it to draw many figures.

    It can also usually be used to edit or combine (encapsulated) postscript and pdf figures if you first convert to Adobe Illustrator format via pstoedit and Ghostview. http://www.pstoedit.net/pstoedit
    http://www.cs.wisc.edu/~ghost/
    (Unavailable fonts and unusual characters can cause problems)


  4. Bill    3841 days ago    #

    Illustrator is horrible. Quite powerful, but monstrously un-intuitive, and so spendy that I don’t think you’ll have happy collaborators if you do convince them to cough up for it!

    Unfortunately, I have not found a good alternative. I’ll have to give Inkscape a try.

    Some of these might be of use:

    http://microsoft.toddverbeek.com/present.html

    and I keep meaning to try out Zoho Show.


  5. Andre    3841 days ago    #

    Thanks for the tips. I will definitely check out Inkscape soon. The screen shots look nice at least.

    Bill, despite its being horrible, do you use Illustrator for your figures or something else?


  6. Pierre    3841 days ago    #

    I use Inkscape. It uses the SVG format (which can also be generated by some other program or created from scratch with a text editor).
    This SVG can then be embedded in web pages or in a slideshow such as Slidy


  7. Fred Ross    3840 days ago    #

    I make my graphs in R, where I can actually use a lot of Tufte’s innovations.

    But for figures that aren’t plots of data, I do something strange, something unheard of: I hand draw them with pen and ink and drafting tools. I sketch in the areas for text and any inserts, then scan it in, and add the text and inserts in GIMP. This means I’m stuck with raster graphics for these things, but I just scan it at a sufficient resolution for all practical purposes.

    This has a couple advantages. First, if you’re just throwing circles and lines around, it’s easy to not worry about what exactly you’re drawing. When you’re faced with a blank piece of paper, all the things you don’t know about the physical structure of what you’re drawing come home to roost. Compare this diagram of mycobacterial cell wall to my drawing (and this is not one of my better diagrams — I didn’t have proper tools to hand when doing it). The peptidoglycan is a disordered mesh, much like vulcanized rubber. The number of connections between arabinogalactans and mycolic acids is correct. There’s lots of details like this that you start worrying about when you have the freedom of a pen in your hand.


  8. Bill    3840 days ago    #

    I don’t use Illustrator, not only because I hate it and it hates me back, but also because I’ve only recently had the opportunity to tangle with it (I haven’t had to make a figure for publication in, um, well, let’s not talk about that). If you are familiar with Corel Draw and PowerPoint and so on, you can muddle your way through in Illustrator.

    I am hoping I’ll have a ms to shop around in a month or two — for that, I’ll probably spend a couple of days trying out the options from this thread! I don’t have a good solution ready to hand.


  9. Andre    3840 days ago    #

    Another vote for Inkscape from Pierre. I asked my office mate and he is strongly in favor of Illustrator, but his wife is a graphic designer so he has professional tech support 24/7.

    Fred, I like the drawing and I really like the idea. Phil and I talked about it once, but given my lack of artistic ability, I’ve never done it. I have often thought it would be great to have someone like David Goodsell to do all your graphics for you.

    Bill, good luck with the paper and please let us know if you find something you like!


  10. PhilipJ    3840 days ago    #

    I would also love to be able to draw figures, particularly after a talk here at SFU given by Raghu Parthasarathy, now a faculty member at the University of Oregon. His talk was on membrane pattern formation, and had lots of beautiful hand-drawn figures like these on his UOregon research website.

    Like Fred, Raghu told me after the talk that the figures were hand drawn on paper and scanned in afterwards. Very cool.


  11. Black Knight    3840 days ago    #

    I tend to use Photoshop and Appleworks or MacDraw.

    So, no help to you laugh.

    Actually, most of my illustrations tend to be protein structures, so PyMol, then label and stuff in Photoshop. Last time I made a poster I did it all in Illustrator (yes, expensive, powerful and non-intuitive) and it was very, very pretty.


  12. janet    3839 days ago    #

    I agree that Illustrator can be a bit of a monster to learn, but is worthwhile and the best of the bunch (I think, anyways) when it comes to vector art.

    For most of the purposes you need, though (image alignment, labeling…) Photoshop is great, and you can do hand drawings as well. Once you have layers figured out, it’s a piece of cake.

    What can I say, I’m a sucker for Adobe products.

    Not to be a walking advertisement for Adobe, but have you seen Adobe’s 3D pdfs? I’ve made some 3D biochem models with this, which can be opened with any current version of Acrobat.


  13. PhilipJ    3839 days ago    #

    Wow, Janet, those are some fantastic images and animations! That’s the real advertisement for Adobe products, seeing all that wonderful stuff. (And I love your domain name too).

    Maybe we’ll tap you for a Biocurious header image sometime in the future. :)


  14. Janek    3839 days ago    #

    Note though that those 3D PDFs require Acrobat Reader 8, while the newest version available for Linux is 7. Also presumably none of the other PDF readers, including the one built into Mac OS X, would support them so overall they sound like a pretty bad idea to me…


  15. fishcake    3838 days ago    #

    the learning curve for illustrator is steep, but the payoff is good. cost is high for individuals, but lots of institutions bulk-license the adobe programs, because they are popular. you may be able to get it on your box for ~free. i recommend scientists take classes in using illustrator and photoshop. it is not a waste of your time! presentation and publication is one of the most important aspects of your work, so learn to do it right! powerpoint is NOT your best friend—design your masterpieces in another program. my 2 cents :)


  16. RPM    3837 days ago    #

    I use and love illustrator. The learning curve is steep, but once you figure it out, it’s very powerful. I make all my posters in illustrator, and I edit graphs and figures in illustrator for publication.

    One of the nicest features of illustrator is that you can import images created using other programs (powerpoint, excel, R, etc), and they are converted into vector format automatically. That makes them easy to edit/touch-up in illustrator.

    The only thing powerpoint is good for is some of its default shapes, which can be imported into illustrator (and become vector based).


  17. Nicolas Merle    3815 days ago    #

    Although the first few images will take one or two hours to do (without anyone around helping you), CANVAS (both available on Mac, PC and even Kubuntu) is definately a program with a lot of potential.
    Quick modifications to already existing images are made possible too. In the latest version I even noticed a good link between powerpoint and canvas (just double-click on the imported image in powerpoint and you’ll be able to change it immediately in Canvas, just remember to save a the end!), hence making the latter even better for images used in presentations.
    One downside is the price, luckily my lab provides it for us (although some undergrads have told me that you can find a cracked/illegal version of it easily).


  18. Yonemoto    3808 days ago    #

    Inkscape. Hands down. It’s free, and there are very few things you can do in Illustrator you can’t do in Inkscape. Also, you have the direct ability to modify XML, which means it’s very esay to make your graphics tidy.

    http://www.scripps.edu/~ityonemo/codon.svg

    (incomplete)


  19. Victoria Càceres    3707 days ago    #

    I came here by mistake, but i`m happy that i did and read your recent research, i almost forgot, how exiting and challenging science is. I`m particularly interest at entomology insects wings nanoestructure.
    I will mark this blog as favorite.
    Cheers!
    Victoria C


  20. Ragini    2986 days ago    #

    Hi, Can anyone suggest a good program for creating figures from Analytical ultracentrifugation data/screen dumps?
    Thnks
    Cheers
    Ragini


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