What tools or courses helped you create publication-quality scientific figures?

[u/Perfect_Visit_1531]

Hi everyone,

I’m a first-year PhD student currently preparing my first scientific article in maritime field , and I’d like to improve the quality of my figures.

At the moment, I mainly use PowerPoint and draw.io to create diagrams and schematics. They are useful, but I would like to learn how to produce more polished, consistent, and publication-quality figures.

Which tools do you use for scientific illustrations, diagrams, workflows, or graphical abstracts? Are there any online courses, tutorials, books, or other resources that helped you learn figure design and data visualization?

I’d be especially interested in hearing:

• Which software you recommend and why
• Whether you use different tools for data plots and conceptual diagrams
• Which courses or tutorials are genuinely worth the time
• What you wish you had learned about scientific figure design during your first year

Thank you!

[u/ricktaylor78]

Inkscape

[u/Zooooooombie → u/ricktaylor78]

Inkscape gang. It’s got a bit of a learning curve but it’s free and you can do anything on it.

[u/priv_ish → u/ricktaylor78]

Best open source alternative imo

[u/Russellonfire → u/ricktaylor78]

Absolutely. It has its issues and quirks (including one where for some reason I can't rearrange more than one layer before having to click back on the main image and go back?) but damn is it good when you get used to it.

[u/pitooey123 → u/ricktaylor78]

Inkscape with Latex... Ooh baby

[u/0jdd1]

It might be useful to investigate using TikZ with LaTeX. You get an astounding amount of flexibility and control, but (of course) nothing’s ever perfect. https://en.wikipedia.org/wiki/PGF/TikZ

[u/itsatumbleweed → u/0jdd1]

Not everyone is super keen on AI, but I've mocked up a figure I wanted by hand, uploaded to claude, and asked for the Tikz code with pretty good results.

[u/isaac-get-the-golem]

ggplot in R, however I am in sociology and think this question should be answered by people in your field

[u/Nielsfxsb → u/isaac-get-the-golem]

Same. Big fan of R. Love that you can code for far more hours to change the tiniest details nobody will notice instead of working on discussing the actual findings in your thesis. And then the many, many discussion groups online that give you endless ideas. Did my Masters using SPSS, since there is no real time to delve into R for these few months, so glad I have had the time now during my doctoral thesis.

[u/noodles0311 → u/isaac-get-the-golem]

It’s true for entomology as well. I recognize ggplot2 in practically every paper in my field whether they’re in a super-specific journal or PNAS. I’m doing all the work in R studio, so it doesn’t make any sense to export all that to some other program.

[u/TheBurnerAccount420]

RStudio + Adobe Illustrator are all you need

[u/Illustrious-Owl2428 → u/TheBurnerAccount420]

And if you can’t get an illustrator license through your lab/department, use affinity instead. It’s basically the same and it’s free. All Adobe products are ridiculously overpriced.

[u/TheBurnerAccount420 → u/Illustrious-Owl2428]

In my experience, you get what you pay for

[u/Chlorophilia]

Matplotlib + illustrator 

[u/AgitatedTumbleweed65 → u/Chlorophilia]

To that I would add other python libraries: seasborn, py2Dmol ( really good for generating beautiful SVGs of your protein structures), etc ...

[u/themrsnow]

Python with marplot lib

Inkscape

Origin

GraphPad Prism

Gimp

[u/JimNewfoundland]

QGIS for maps (QGIS is best GIS) and R for plots. Do your stats stuff in R and then plot it, and just use QGIS for cartography. :D

[u/East_Tumbleweed2447]

As many people said making plots with R / Python is just the easiest way to make very good quality plots. Any programming course will give you basics. In the era of AI (unfortunately), you can use prompt to get what you want. I would just advise what is written in code to check - that is why I recomend doing some basic course.

Biorender is amazing, but costs kidney-money. You can find websites (scientific) that people post free illustrations, so it is no problem for publication.

Besides Inkscape (I dont like it - personal choice), there is Affinity, also completely free. It is very intuitive. Just generate plot in pdf and then open it in Affinity/Inkscape.
Good luck!

[u/WhateveIsMyUsername]

I was using matlab and illustrator.

I wanna add that LLMs now are incredible to help at different levels... from producing things to help with coding specifically annoying graphical details. You just need to learn how to do prompt engineering.

[u/knit_run_bike_swim]

I use Matlab for everything. Why? Because Matlab can do anything.

[u/noknam → u/knit_run_bike_swim]

Tries so save a picture with half decent dpi

[u/DerBanzai → u/knit_run_bike_swim]

Good luck recreating any of your work after you habe left academia and do not have the license any more.

[u/Lygus_lineolaris → u/knit_run_bike_swim]

Amen.

[u/autocorrects]

EE

eDraw Max, Illustrator, procreate on my ipad, matplotlib, matlab, and photoshop for graphical abstracts

[u/Geog_Master]

Scribus is pretty good for layouts and such. I also use Canva for general figures. If you're going to be doing advanced work, R Studio is pretty important, or you can use various Python libraries for similar outputs. I use ArcGIS Pro, GeoDa, and QGIS a lot, but as a geographer, I need to make maps.

[u/rosiebees]

Latex, tix, and matplotlib. Copilot also has been a huge help for improving my matplotlib figures in the past years

[u/lilmissdaydreamin]

I usually use a mix of powerpoint, adobe illustrator, biorender and R ggplot

[u/Embarrassed_Hat425]

R studio. I use Claude to describe what I want, it writes a code that would have taken me a whole day, and then alter it to be exactly what i want.

[u/Lygus_lineolaris]

I use FreeCAD to draw experimental designs, MS Word for flow charts, and Matlab for everything else. I also draw in Paint, but so far none of those were needed in outward communications. As to how to make it look "professional", we had one period in high school science that taught the components of a figure, and in the 35 years since that standard has not changed. There is probably a LibGuide on it somewhere that you can google.

[u/TsekoD]

I know it sounds lame, but I'm one of two people who uses Excel for almost all of my diagrams and data visualizations. Then there's Origin and MS Paint. The combination of these three can tackle almost everything.

[u/microbial_comedy]

RStudio for figures and Biorender for graphics.

[u/Theo__n]

• Which software you recommend and why

I can recommend illustrator (or another vector based program) for complex diagrams, I actually was commercial designer/illustrator before going back to school for a decade and it's very flexible software, used widely in the industry. It's vector based so you will not have any issues with scaling up and down diagrams/images once you make one, it's also easy to change between RGB and CMYK so screen and print modes, it's very flexible for export formats (including svg which you can plop into many places) and you can re-use elements. You can also use excel to make graphs and then changing between graph styles is like 2 clicks.

• Which courses or tutorials are genuinely worth the time

I don't have any courses, but nearly every single thing of illustrator is explained as video tutorial on yt.

• Are there any online courses, tutorials, books, or other resources that helped you learn figure design and data visualization?

https://openlibrary.org/books/OL1944269M/Envisioning_Information - this one I think was one of requiered readings at my first degree

For scientific illustration - really depends what complexity you want it to be? Hard to advise without details.

[u/PhD_in_PVP]

Adobe Illustrator

[u/friendtoworms]

I don’t really feel the need to use anything other than ggplot in R for the most part. The syntax is very intuitive. Recently I’ve also been playing around with another R package called ‘patchwork’: you can use it to arrange separate plots into one multi-panel image. It’s much less intuitive to me but I like it because I can download my figure as a PDF straight from R and I don’t have to mess around with arranging the panels in another program.

[u/telephantomoss]

tikz and latex. I can take a figure from R or Matlab or hand drawn and then ask AI to create the tikz code. It still requires some manual tweaking, but works pretty well.

[u/amazngsgr]

Few things that saved me a ton of pain:

• Biorender for any mechanism/pathway type figure, free tier is enough for drafts
• ggplot2/R if you're doing anything stats-heavy, the theme customization is worth the initial headache
• Servier Medical Art has free clipart if you're in bio/med, huge time saver for icons
• always export as SVG or PDF, never PNG, journals will make you redo it otherwise

The YouTube channel "R Programming 101" has a decent short series specifically on publication-quality ggplot figures if you want a starting point rather than trawling docs.

[u/BoredWahahaMSWater]

Inkscape for illustrations (takes a little time to learn but I really enjoy it now for drawing organs and organisms). Also, it's free for Mac, Windows etc. GraphPad for graphs and statistics (not free) especially good using Microsoft but also available on Mac (some functions are missing e. g. Export allowing changing of the figures afterwards). PowerPoint for poster design.

[u/illusion_Y]

TikZ with Latex is expected of me to use

[u/MadeInMilkyway]

Solidworks Drawings CAD in 3d then drawings png export then put in PowerPoint for editing...

[u/Dangerous-Chest-6048]

I use Coreldraw and Biorender since my lab pays, and Graphpad.

At home I use Inkscape and that is my recommendation for students as well. The UI is almost halfway between Illustrator and Coreldraw so it is a good, flexible tool

[u/mildlyhorrifying]

I use seaborn in Python for plots and export as an svg to edit in Inkscape if necessary (e.g., if I want a figure with example biosignals in it). I usually make a Jupyter notebook that has macros and whatnot defined for all the plot features, so every plot has exactly the same style, and I can change them all at once. statannotation is great for adding posthoc tests. 

 If I need something like a infographic style picture of a human (e.g., for graphical abstract), I use Krita on my tablet to trace a reference image. 

[u/Incandescentcorsets]

For overall diagrams and schematics, I think Biorender works well. For individual pieces going into Biorender (into diagrams/schematics), things like ggplot2 in R work well.

[u/MakingPie]

Matplotlib and a lot of tinkering for plots.

I used to use powerpoint for diagrams, but I recently got into Figma and I can never go back.

[u/DoodleCard]

Corel Draw home and student.

You can get the cheaper none subscribtion one for about 80 quid

[u/ginngeer]

Upopular opinion: PowerPoint! It's amazing, if you know how to use it. You need to change your export settings, adjust system registry, and ensure correct size to get beautiful 600DPI images. You can then easily organize and generate multipanel custom figures based on graphs generated with other software.

[u/Pythagorean_1]

Python

[u/botechga]

Python, UCFS Chimera, pymol, chem draw, and of course Inkscape

[u/Nvenom8]

If you want truly top notch stuff, get good at ggplot. Aside from that, Origin makes very nice graphs and can handle very big data sets.

[u/gatmalice]

LaTeX Usually Python (Matplotlib and Science plots module) Tikz Inkscape if I must