I am learning Adobe Illustrator for this reason.

Inkscape, Blender, Matlab, Octave, Xfig, GIMP, Povray and PBRT.

When I want to plot data, I usually go to Python's Matplotlib, the R suite, and sometimes Matlab. To draw 2D graphics in general, PGF/TikZ is my first choice (it takes some work to start with, but once you get used to it the results are amazing!). For 3D (and 2D) graphics, Asymptote is an excellent choice. For specific cases I've already used Blender.

I like Solidworks (Photoview 360), which has automated 3D rendering functions. You can see an example in Fig. 1 of my prior publication (attached).

Article Unidirectional mechanical cellular stimuli via micropost arr...

Surely Adobe In-design with Photoshop and illustrator for 2d (imported from engineer and mat program) and press. In 3d visualization Autodesk 3ds max (if are enought skilled) and Nuke for compositing.

Octave, Matlab, gnuplot can provide you with good plots, which you can export as SVG and then finalize with Inkscape. Especially the TexTex plugin is usefull, if you want to have equations (signs) in your drawing.

For example: an equation bent along a sphere:

The first question is whether you want to use open source or commercial software. For plotting and analyzing statistical data I use Origin. As open source I would recommend Gnuplot but that is mostly console based. For 2D and 3D graphics you can use Dia as free source program it is intuitive to draw vector graphics and allows saving files as .jpg .ps .eps .tiff and several more file formats.

As already said.

This software are more related to computer graphic but can be used for scientific purpose. Especially, you do have plugin for blender to visualize molecule, protein, enzyme, and DNA. All the free software are supported by a large community of users, with large amount of on-line tutorial and forum.

Don´t be shy and try them, it´s free and good. The best way to find a software suit you, it´s go to google and search for something like "XXX open source", "XXX free software", "XXX GNU" (XXX is the name of the software you are looking for a free open-source version).

I agree than the open-source version have less function and bugs a little bit more, but it can also save a lot of money and time as you do not have to fit the software in your tight project budget.

Gimp (a free photoshop-like software):

http://www.gimp.org/

Blender (a free 3D-suite very high quality but not easy to use):

http://www.blender.org/

BioBlender (a free plugin for Blender to visualize molecule):

http://www.bioblender.eu/

eMPV (a plugin for blender for molecule/cell visualization):

http://epmv.scripps.edu/home

Inkspace (a free CorelDraw-like software):

http://inkscape.org/

You have also plenty of free scientific software for specific scientific visualization like:

Paraview (the most well know software for visualize very complex 3D/4D dataset):

http://www.paraview.org/

Quatum GIS (free GIS software for geographical dataset visualization):

http://www.qgis.org/en/site/

MeshLab (free software to manage very complex point cloud):

http://meshlab.sourceforge.net/

CloudCompare free software to manage very complex point cloud):

http://www.danielgm.net/cc/

A Classic for data presentation is imho IgorPro by wavemetrics, http://www.wavemetrics.com/

For 2D illustrations, Adobe Illustrator is a very powerful tool. For 3D illustrations, Google SketchUp is a free software and allows to make some structures of your assembly transparent to highlight features.

A lot of those are good for standard types of figure, data plots, etc., but if I want to draw a clear _diagram_,, unlimited by package designers' assumptions about I should be drawing, I write PostScript (.eps) code. There are often things I want to do, particularly in 3D diagrams, that I have never yet found in a software package.

I don't have to add any other software to the lists that have already been provided. I have mostly used open source software myself for my illustrations. If your illustrations are good mostly depends how well you can use the different tools. Expensive software does not guarantee good illustrations, but learning your tool does. It is more important that you keep your illustration as simple as possible without leaving out any details.

To have a good quality for the final print the format of your file is more important. First, you should try to do your illustrations as vector graphics. They scale well to any resolution. Many people already suggested Inkscape. It's native format is SVG (Scalable Vector Graphics), but that cannot be embedded into a document directly. EPS and PDF have support for vector graphics, but can also just include bitmaps (i.e. a per-pixel representation like in a picture/image). Make sure that if you export to one of these formats that the result is still a vector graphic. The nice part of Inkscape is that you can include LaTeX directly into you image. The best part of this is that your final image will use the same font as the rest of the document (even if you are not using formulas in your images), which looks a lot nicer. (This is restricted to the case that your document is in LaTeX anyway.)

If you have real images, not vector graphics, than you should use a file format that is loss-less, e.g. PNG. JPEG by design looses some data during compression and might show compression artifacts. Your images should at least have 300dpi (dots per inch) for printing. Remember that scaling and paper format will have an impact on this dpi number for the embedded image. 300dpi is a real minimum requirement (think retina displays), but in printing the general rule of thumb is 600dpi for good quality images.

Now, go on, pick your software of choice, learn it, and stick to it. The best software available is the one you know how to use.

Honestly, while your question is about software, the answer is about skills.

This is very much a situation where it is the craftsman, not the tools, that make the difference between good illustrations that communicate effectively, and utter garbage.

Certainly, there are tools that make creating good work easier, and tools that make it harder, but when someone asks "what tools should I use for scientific illustrations", it's almost /always/ the case that they really should be concentrating on the skills. If you've got the skills and can come back with a question of "I'm trying to accomplish X, and the software that I'm using limits me by doing Y - what does this better?", then recommendations for software are likely to be helpful.

Before you get to that point, the most important software that you need to learn to use, is the stuff between your ears. Until you can visualize what you want to accomplish, and know why you're making the design and representation choices in your images, a huge toolbox full of tools is really going to be more of a hinderance than a help.

That being said, for gods sake, whatever you do, don't use PowerPoint...

@William, I wholly agree.

Use the simplest tools you can, to achieve a clearly imagined result.

And avoid visual clutter engines like the graphics in Word or PowerPoint: they can only confuse you and your audience, unless tamed with utter mastery and clarity of mind.

Hi,

I'm a scientific illustrator and frequently create designs for journal covers:

http://portfolio.scistyle.com/filter/journal-cover

For my workflow I mostly use commercial software such as the Adobe Creative Suite (for 2D images: Illustrator). For 3D (such as protein structures) I recommend Maxon Cinema 4D. It is very powerful, yet more intuitive to use than most other 3D packages.

We generally use ACD Canvas for 2D illustrations. It is a powerful tool capable of dealing with many different types of file formats. Although not as well known as illustrator, our experience with this software has been superior.

I use paint .net for working with photos and images ( like sem or fluorescence photos). But for vector graphics adobe illustrator is great. It is possible to do 3d images in illustrator too by turning on the perspective axis, but I find it rather clunky to use for 3d.

Some software that has not yet been mentioned:

- xfig http://www.xfig.org

Good program for 2D diagrams that can save in various formats. Includes LaTeX support.

- gliffy http://www.gliffy.com

This is an online tool for 2D diagrams. It requires a sign in and the free account allows storing up to 5 diagrams. I have never needed beyond 5 at a time and rewrite my old ones when needed.

Also, one can get decent diagrams using PowerPoint and Visio.

It all depends on what you want to do and how proficient you are in any of the programs mentioned. If you're new to graphic design all the above programs have steep learning curves. If you're into graphs I would recommend something simple enough as apples' numbers (if you have a mac), otherwise in my opinion for 2D graphics CorelDraw is a bit easier to learn than others i.e. illustrator. For 3D graphics, probably the easiest program to learn is sketchup but it has a lot of limitations as to what you can do in complex scenes. Try considering Bonsai 3D, not very famous, but quite powerful for complex geometries and cheap as well.

For charts: OriginPro

For diagrams: https://www.draw.io/

For 2D: Illustrator + Photoshop

For 3D: Cinema4D + AfterEffects

All of these can run as a trial (except that for diagrams, which is free).

I want to suggest Flash for drawing and illustration purposes. Thought best is illustrator but flash is easy to handle.

Though powerpoint is also handy. While eps export is not supported yet microsoft has its own emf format which is also only supported vector export in some softwares like MEGA (http://www.megasoftware.net/)

Though most people complain for poor quality image production through powerpoint export feature even if its clear inside powerpoint. This feature is due to low export quality setting as default for powerpoint. Folloe following steps to enhance the quality to 300dpi for best results and it is as good as illustrator for publish quality images.

http://support.microsoft.com/kb/827745

Moreover powerpoint has a default setting that compresses images to low quality on saving. this feature can be turned off by steps in folllowing link

http://office.microsoft.com/en-in/powerpoint-help/turn-off-picture-compression-HA010355184.aspx

still the max resolution powerpoint can support is 220 ppi or 220dpi.

But powerpoint is way handy and known interface for normal users.

It has been well argued that PowerPoint contributed to the Columbia space shuttle disaster: http://www.dryeyezone.com/encyclopedia/mgd.html.

It is a way handy and known method for dumbing down both the presentation and the presenter -- and increasing the dpi does nothing to fix that.

@Tim Poston. COuld not understand any of the words told :D

There are many graphics programs out there - I agree that one should use the one that you are most comfortable with.

On the open source/free side, I can reccoment OpenOffice/LibreOffice, which has a powerful graphics package included (2/3D drawings & dimentioning, flow charts etc.. You can try Google SketchupFor 2/3D drawing or Inscape, for vector graphics.

Most of these programs are capable of producing excellent results.

For vectorial 2D I have good experience with CorelDRAW, as a cheaper alternative to Illustrator. And Inkscape is even free, but it is a bit rougher in the implementation details. For 3D, it depends. As an architect, apart from SketchUp, I tend to use ArchiCAD for building models and Cinema4D for rendering, but organic models with double-curve surfaces can be created in Rhino.

In most cases, though, it's mostly the artist that is the essence to get powerful, convincing images, regardless of the tool used. And in many cases, this might not be the actual scientist who developed the paper.

To me, the tricky part is getting a clean and visually pleasing image directly outside of the data. E.g. spreadsheet data that is turned into a non-standard Excel Chart as it stays connected to your model data. The more "live" your graph is, the more it allows you to explore the data. I often try to avoid freezing the data just for illustration purposes.

Inkscape (http://inkscape.org/) is free and based on Vector graphics. Lots of formats to save, including .tex

For very simple designs you can also use drawing capabilities in Microsoft Office (Powerpoint etc)

Corel Draw graphic suite satisfies my need for vector graphic and images, Origin PRO for graphs. So, this two should be my suggestion.

I liked the ACD Canvas. Together with MS Office, the inbuilt charts and graphs of MS Office, treated as vector inside canvas, makes it perfect combination cause mx people are handy for collecting and presenting data nearby ms office i guess.

Safdar,

You can produce excellent quality graphics with just about any software, but you need to know how to use it, and have an artistic side and "an eye" for graphics. This is really the deciding point, the software is just a tool. It's all a matter of how much time you can dedicate to learn the program and then stay up to date.

That said, I personally try to stay away from Office, but I've seen decent graphs made with Excel, even in 3D (but avoid the default colors!). NEVER use powerpoint to create graphics.

For sketches and vector graphics, there are multiple free and non-free programs out there. I find Inkscape (free) easy to use, and more intuitive than Illustrator. To improve raster graphics, Photoshop is the standard, but there are also alternatives (GIMP, PaintShop Pro, Paint.net...). Avoid jpeg as an intermediate graphics format, it's lossy.

If you do 3D work such as solid modeling, numerical simulation and things like that, most modeling software allows you to import a background graphic to present your model in a "scene".

For "artificial" 3D sketches, I've seen people use Maya, 3D Studio, Blender... all these are difficult to learn properly (especially Blender), but once you know them you can literally do magic with them.

The bottom line: choose ONE program that will do the job in each category, and learn to use it properly. Which one you use is less important than how you use it.

Hope this helps,

Fernando

I agree with Fernando. I use R statistic (http://www.r-project.org ). I bought a book ("Using R for Introductory Statistics") and read stuff online and with that I have been able to generate all my plots and stats. It suffices to me in that front. For illustrations in 2D I use Word or Powerpoint. For 3D I use 3d Studio Max. They have some free licenses for students (http://www.autodesk.com/education/student-software), if that is your case.

Despite the hefty price tag, nothing beats the most widely used professional illustration software, i.e. Adobe Illustrator. It also integrates seamlessly with adobe indesign which is far superior than anything else I tried to assemble figures from multiple panels. It also integrates with photoshop for enhancing figure panels. The major drawback is the limited integration with statistical packages that output graphs, which requires a reasonable amount of playing around to get font sizes right.

Be mindful though that the learning curve for adobe software is reasonably steep and particularly long. Nonetheless the Internet is full of tutorials that explain how to do every single thing.

There is a lot of drawing and illustration software, but unfortunately I must to say that almost all of them have limitations. The important thing is that you have some artistic or design skills to get a nice figure / image. I prefer to use Adobe illustrator for the most part. You can see some of my figures on my website.

http://www.fbscientificartdesign.se/en/science-17179657

I recommend having the graphics done by a professional graphic designer instead of buying software.

Most professionals work with the Adobe Suite, Illustrator is used for 2D-illustrations. For 3D-images Maxon Cinema 4D, Maya or 3DSMax are most popular. But again, the best tools won’t automatically produce high-end graphics.

Safdar,

the chosen software will depend much on which kind of illustration you need.

I use Adobe Illustrator in a daily basis, for 2D illustration.

If sometime I need something done in 3D, I prefer to use Blender.

Both have a steep learning curve...

You may also take a look on the tools available for free in Google Drive.

Hi!

I usually prefer a combination of Origin Pro (for graphs) and Microsoft Visio (for simple, schematic 2d drawings). For 3d stuff i recommend a CAD-Software (SolidEdge or SolidWorks) because you can create close to photorealistic images with it.

I can also recommend Gimp for image modification, since it is almost as powerful as Photoshop and for free!

You may also want to have a look at the ADOBE Creative suite, Illustrator is quite powerful and also InDesign is very good for posters.

Cheers,

Christian

For 3d stuff I do _not_ universally recommend a CAD package, precisely because you can get regrettably close to photo-realism. A photograph is not a diagram: It is usually less comprehensible.

This is particularly clear in medical journal articles. Actual photographs are easily made and inexpensive, and useful, but every research hospital employs at least one skilled medical illustrator able to create drawings that communicate the anatomy and procedures involved.

Similarly, a circuit diagram is usually clearer than a photograph of a circuit.

Photo-literalism is too often used as an alternative to actual thought about visual communication. The results can be dismal.

I prefer 3D. In the cartoons, I made a 3D personal vision of the targets for antimicrobials in a bacterium and a bacterial cell wall in G+ bacteria

Antimicrobial targets.. (in spanish :-))

To do that, you can use Blender (free software) or a CAD package, the results are similar, but requires some skills. once you have some experience you can made things like these in 1h, more or less. if some of you needs something, don't doubt to request me something of this type, I will be charmed of making it (free of course).

Greetings from the sunny Spain

For statistics and graphs, MATLAB or Prism

tx for all, i'm hight skilled in 3d graphics for videogames and visualization, also in 2d for character. Very interesting, if someone need an illustration for pubblication or arcticle mail me, i try to realyze for free, i want to do a bit training.

List of software I use for creating figures/graphs for scientific publications:

Plotting and combining graphs - Origin

Image analysis - NIS elements / Image J

3D images - 3ds Max or Blender (Blender is an open access software)

Occasionally I use Gimp or Powerpoint for combining multiple images.

There are a lot of people using Origin, for those out there that do not have a license there is an open source software called SciDavis that very closely resembles Origin and produces good quality plots. As for 2D illustrations I like to use Adobe Illustrator and Inkscape. I have used Blender and 3ds Max before and found 3ds Max a bit more intuitive but I have not had the need for many 3D illustrations so I have not tried many softwares in this area.

I usually use: Origin, Gnuplot 4.6 for plotting.

Blender, Gimp for illustrations and of course Latex for text... :)

Before LaTeX learned to import graphics in the 1980s, I drew a bunch of figures with the LaTeX 'picture' environment -- quadratic splines and all. I thank Ganesha, god of innovation, that I will never need to do that again.

As a rule of thumb, if a drawing tool is from Microsoft it is the worst available: but Gates-evil never came close to LaTeX graphics.

It does get better.

... Your question has a rather wide range ... What are you up to illustrate? And what is the purpose of the illustration? Could this give a hint to the tool you could use? Please let me know. Friendly regards

... do I get you right, that you use a set of standard packages for 3D modeling and for image processing you use Illustrator? How do you transfer the graphics from the modeling tools to you illustration tool? And which objects do you model in 3D?

with 3dsmax is possible to model or sculpt anythink. Normally the output of a 3dprogram is a render. Than render will be imported in an illustration program.

Having a chemistry background I presume your request might be be the visualizing of various molecules. In that regard, there is a modifier in 3D Max called "lattice" that you may find quite useful.

You basically draw and adjust a vector line in space with points (vertices) where every atom might go, then you apply the lattice and it will put balls onto each point.

For graphical presentation of processed data, I usually use GraphPad Prism that can generate professionally looking graph and also has the ability to run statistical tests. You can also arrange generated plots in Prism to save you the hassles from arranging them in Adobe Photoshop. For microfluidic design, we usually use AutoCad for 2D drawing. I'm not very familiar with 3D illustration but as mentioned by others, 3ds Max is commonly used.

GIPM or INKSCAPE is very good for drawing and diagrams. For flow chart Microsoft visio or E-draw or smart draw is good. For technical drawing solid edge ,autocad, labview etc, are very useful.For plotting graphs sigma plot or origin can be a good option.

Thank you all..Your comments and suggestions were very useful for me. I have adopted Illustrator for now but someone told me that Rhino 5 and Solidworks are very useful for 3D models.

Thank you very much everyone once again.

If you're interested, I have both my MS and BFA. I studied Graphic Design at the University of Michigan and then returned to do my Master's at The School of Natural Resources and Environment. Given both these backgrounds, I have a high interest in graphic design for environmental and sustainability related pieces and scientific illustration. You can check out my website at http://www.behance.net/lindsaybienick

and I can send you some examples of my drawings (which aren't posted). My most recent work involves designing for the Detroit Climate Action Collaborative, and designing the lesson plan layouts and book for a soon to be published Michigan Forestry Climate Change Curriculum Guide Book. If you are interested, just email me at [email protected].

Use techplot sofrware

Inkscape

If you have to deal with molecular structures - Pymol (http://www.pymol.org/). It can generate good quality images and is used for molecular journal covers preparing http://pymolwiki.org/index.php/Covers

If you are talking about "scientific illustrations" I guess you need a professional illustrator or graphic designer to accomplish this task. I suppose you want to create non-data visual elements, but stories of science, then you need to create contents form scratch. There is no formula for this. Some softwares: 2d Adobe Illustrator, http://www.blender.org/ for 3D, or maybe you can use some tools for storyboarding, such as: https://www.toonboom.com/products/storyboardpro, https://www.celtx.com or http://www.powerproduction.com/storyboard-quick-software.html with built-in avatars and scenes.

It depends on the type of visualisation needed, the program you use for data analysis and your input material. Ina addition to that your level of expertise and the time you have to invest in passing various learning curves.

(1) For quick and dirty, and for almost all the basic stuff (i.e. images, flowcharts, basic graphs etc. ) I would recommend powerpoint 2013 for the following reasons :

A. Almost no learning curve as it is one of the most common graphic suites available.

B. The new design has built in capabilities that are both user friendly and easy to use.

C. If used in a per figure fashion you can adjust the figure dimensions to achieve a good flexibility.

D. All the work you invest can be used later on for presentations and posters seamlessly.

(2) For more advance figures containing multiple elements and graphics extracted using various analysis flows, the combination of adobe photoshop (for image preparation) and adobe illustrator for figure assembly and any type or vector is the fastest payable way (although it will cost around 150£) and the free alternative is gimp and Inkscape (both open source programs).

(3) For 3D visuaizations, it depends on various parameters (e.g. for imaging i would use Amira or freesurfer, but for simulations Matlab or a per discipline designated software and for self created models and animation either MAYA or its open source alternative blender are the best but cinema4D is probably more intuitive )

Hope it helps

Eyal

For visualization of 2d or 3d scientific data I recommend tecplot. (www.tecplot.com) For 3d illustrations with shading and textures a CAD program would be the right choice. Rhinoceros has a good value for your money.

I recommend a designer :) the software is not the main. You are the expert in the contents. Do not lost time in the representation, use it in the idea.

I agree with Ariane, but there are a lot of bad (lazy, incompetent, etc.) designers out there. I have been involved in several projects where someone was hired for their design skills and never delivered, refused to make changes to their initial design, refused to provide final document files so that changes that they refused to make could be made, asked for more money after putting in what looks like a few hours work, download their designs from the internet, etc. Obviously there are many excellent design professionals as well, but I recommend finding a designer whose work you like and going to them directly. Start a "swipe file" (a cardboard box or folder on your computer where you collect samples of excellent designs of all kinds that you can browse when you need ideas). Pay attention to informational graphics in other publications (newspapers, books, etc.) and save copies of the work and the designer. One of my colleagues designed informational graphics for newspapers before he became a professor a few years ago (http://ploubere.com). He has done some excellent work. Indeed, many of the newspaper informational graphic designers are excellent, I included their work in a chapter on design and infographics in my Public Relations Writing book a few years ago. Being able to visualize something well and create a compelling graphic is not something most academics are trained to do. Get someone to help you if you have a reliable friend or have a budget for it. Another of my colleagues, a very successful author, gives a graphic designer friend a cut of his electronic book sales. Some of his projects are netting him a thousand a month (100 for his designer) -- that's good pay for a book cover to receive "forever." If co-authorship is important to someone creative (someone in a design college perhaps), they might be willing to help for free. Also, design students interested in building a portfolio are also potential allies.

I remember when worked for United Space Boosters a while back when the Space Shuttle was still flying. An old technical illustrator taught me so much about doing illustrations. He had matured through doing hand drawings on a drafting table to using a state-of-the art CAD workstation. The best thing that I learned from him was to use the application that did the most for you with the lease amount of effort. Often times he would use a simple program even though he had access to much more powerful applications.

I am with Eyal, I do most of my technical illustrations on Powerpoint. I am certified in SolidWorks and Inventor, and have also used 3D Studio Max. Both of these have very steep learning curves and you need to understand drawing theory and design intent.

If I need 3D photorealism and technical accuracy I will using SolidWorks. If I need photrealism and needs to look good but not be technically accurate, then I would use Studio Max.

Whatever you use, the aspect of design iteration was always important for me because often you may need to change something in the illustration or tweak it. For those reasons, a vector based program with layering ability is the way to go. Corel Draw is another good app. The design tree in SolidWorks and Inventor is nice for revisions.

I would strongly agree to Mr. Gärtners view: collaborate with a graphic designer. You will get much better results and save lots of time (and frustration)

For the best graphic Design the CATIA, and SOLID WORKS as well as PRO E Software are very good also you can analyses(Simulation, Optimization, stress analysis, Machining etc.) your Part Model in CATIA .

You can also use the MATLAB Software for doing advance research in your field.

If we want to publish our Research Paper in Higher Grade Journals it is necessary to have a license of that particular Software which we have used in our research paper.

I can highly recommend SmartDraw for anything 2D-related.

Depending on the exact field and what you need to illustrate.

Rhinoceros 3D is good for quick machine/technical CAD illustration.

Igor Pro, once you get used to the idiosyncratic style. The command line interface that duplicates pull-down menu commands makes it much faster to do repeat analyses since you can copy-paste and only need change the data file names. Total control of the graphics and proper image analysis. Though if I were starting again now, I might just use MATLAB for everything.

Answers above have covered many of the great data visualization software packages available. I will discuss 2D and 3D illustration.

Most high impact journals have staffs of professional illustrators (of varying quality) that primarily use the print industry standard Adobe suite of products. This means Photoshop for photo adjustment and raster-based illustrations. These files are imported into Adobe Illustrator for text labeling, graphics (leader lines, graphs, layout of illustrated charts), and vector art. Most "inside" art for publications, i.e., didactic figures, are redrawn by the illustration staff, based on the illustrations sent by the author, using Adobe Illustrator, because vector art is generally faster (cheaper) to draw and lends itself to clarity, simplicity, and reproducibility. As a broad and very incomplete/inaccurate oversimplification, you can think of Photoshop as being useful for digital painting and Illustrator as being useful for contour drawing (outlined shapes with flat or gradient colors), but of course that line is incredibly grey and both applications have thousands more uses.

If you submit a clean, professional illustration for inside art, many journals will opt to use it as-is. If your survey the high impact journals, you'll see that cover art is a different matter entirely. Some journals use only one illustrator or small collection of illustrators/artists/photographers to produce covers in a similar style (often internal staff). Most journals, however, use some mix of professional art (commissioned either by the journal, or most often by the PI of the submitting group on a gamble that a professional scientific illustrator will give them a "leg up" against the other competing covers), art created by the researcher, internal art, stock art (Science often uses stock photography), abstract or highly metaphorical art (Cell shifted in this direction, towards cool abstract paintings, starting in ~2007) often created by professional non-scientific artists, to comics, etc.

I highly recommend following the advice others have posted– of hiring professionals to (or letting the journal staff) do your illustrations. In the USA there are two major organizations (with some international members as well) of scientific and medical illustrators you can go to to hire a pro. You can find links to portfolios, etc at the Association of Medical Illustrators http://www.ami.org and the Guild of Natural Science Illustrators, http://www.gnsi.org. Be prepared to pay. Medial Illustrators have masters degrees in the subject and can provide significant input to improve the clarity and beauty of your life's work. You will not hire such a person to redraw your spreadsheet graphs, but instead will bring them on to clarify a complex story, put your data into a larger context, or work on your cover submission. Cover prices can range from a few hundred US dollars to several thousand.

If you or someone in your lab has a knack for art (or even just an enjoyment of creating art), then you should certainly try your hand. If you want to get into creating such work yourself, I've taught photoshop and various 3D software packages to researchers for many years, so I can offer a bit of advice on software choices, etc. My colleagues and I have started to assemble a discussion group around this topic of art in science, following on a presentation we gave at ASCB last year, so I recommend asking any detailed questions there as we try to ramp up and flesh out the discussion. http://www.mesoscope.org/sciviz-careers-tools/sciviz-careers

I've had people use free software in my classes and have explored it myself, but unless you used it on a very regular basis, it tends to be highly limiting- not in its capabilities, but in its usability and intuitiveness. Photoshop is not intuitive either, but after a half day's worth of tutorials or a workshop, most researchers can perform most of the tasks they need quickly and efficiently compared to GIMP, so ask yourself if you have more time or money to decide which route is best. As many others have already mentioned, in 3D, the software package Blender is very powerful and a free open-source project, but it has one of the least intuitive user interfaces I've ever experienced, so unless you are a programmer or plan to do 3D as an open-source hobby, or really really really want to spend $0 forever, I'd steer clear of it. I've seen dozens of researchers get introduced to 3D via Blender and effectively just never touch 3D again because its such a nightmare experience... it doesn't have to be: The package Maya from Autodesk is incredibly powerful- the workhorse of Hollywood, and Autodesk is brilliantly forward thinking offering free 3 year licenses to academics. They also have a new R&D team working on biology specific projects. Maya is powerful, but it also takes a career to learn, so its definitely worth considering if you plan to shift careers into scientific visualization, but otherwise you may prefer something easier. A small majority of us medical illustrators use Cinema 4D because it is pretty much as powerful as Maya, but it is famous for having the most intuitive user interface of all 3D software- its a very clean experience and has a large community of scientific illustrators handy to answer questions specific to scientific visualization (search google groups), however, getting an academic or student license is still a bit tricky and involves registering your entire university before students can apply for licenses, so you'll likely have to pay a few hundred for the commercial version of the academic license, and the "street price" is ~$3,500 US for the full package. There are free demo versions of all of the software mentioned (Adobe, Autodesk, Maxon Cinema 4D, etc.)

If you do 3D molecular illustration, there are many great freeware molecular viewers, and our labs at The Scripps Research Institute and UCSF also develop plugins (ePMV, cellPACK and uPy) that enable you to operate scientific software as plugins directly inside of 3D animation packages like Maya, Cinema4D, and Blender for free. We strongly encourage researchers to get involved, take an art class at your local university, have fun and spread your knowledge more effectively. If you're too busy or not interested, then hire a professional!

MatLab or Mathematics, they are professional math softwares and powerful for scientific graphic

I am surprised that noone mentioned tools like TikZ and PSTricks for 2D and asymptote for 3D. Same strength points of (La)TeX and friends apply also in this context --- program you images and take full control over the output. Moreover, the sources are merely text files which are easy to share and put under versioning control.

Probably some examples are important:

http://www.texample.net/tikz/examples/

http://asymptote.sourceforge.net/gallery/

It depends on the type illustrations that you will be interested in. I use AutoCAD and Autodesk Inventor Professional for the purpose of creating illustrations.

For 2D images, I use AutoCAD. When using AutoCAD I normally create the drawing using “Arial” as the text font and control the line thicknesses as required. I normally use 0.4 mm for thick lines leaving default for thin lines. Once the drawing is completed of the correct size, then export the entire drawing using the WMF option. Windows Meta File option generates the vector image which can be scaled very conveniently in Microsoft Word without any problem. I am attaching a file for your reference with two images made using this technique.

For 3D images, I use Autodesk Inventor Professional. Here any 3D image can be very quickly generated and then a drawing can be created from the model and that drawing can be exported to AutoCAD and then follow the same procedure as outlined above.

Let me know if you need any further information about these techniques.

The work flow I would suggest would be starting with iPython: http://ipython.org/

Then use the matlibplot library: http://matplotlib.org/

Export the various graphics into SVG format and then spruce up in Inkscape: http://www.inkscape.org/en/

If you want to do 2D to 3D (not using the 3d stuff in matplotlib), import the SVGs into blender: http://blender.org

I agree with eric, blender 3d is the best 3d open source software for any illustrations. You may also use deep view from right hemisphere (free software) to import 3d model into powerpoint to show animations or import to pdf to form 3d pdf.

Really it depends what you need and your ability to get most out of applications.. all the software's mentioned above are very nice but usually require expertise. For me, Ms Word can create awesome Flowcharts and Diagrams, you can use MS Excel to easily create Graphs, Charts. Use Photoshop to create illustrations and all sort of diagrams even sometimes Ms Paint is enough if you know how to use your mouse.

I use matlab, Mathematica

matlab figures are great to manipulate and can be save to different types of files

For 2d Inkscape and 3d I use Rhino3d. Blender and 3d Max are very good 3d programs but have a vastly higher threshold to start to generate amazing designs compared to Rhino...

For visualizing data I use matlab save as a vectorformat if possible and do the final tweaking in inkscape.

Usually matlab, powerpoint, GIMP are used in my work.

I am using Inkscape for 2D (vector output, Free, but bit hard to learn), Autodesk Inventor for 3D (easy to use, Free for students, but need to save in raster image-would have loved to get svg directly)

If you want free software with GUI, I agree with Inkscape and GIMP. Nonetheless the results depends on your skills. If you need just 2D graphics (or simple 3D) the most professional solution is IMHO Latex. There are even libraries above the Latex (e.g. http://latexdraw.sourceforge.net/)

Personally, I'm using also Omnigraffle (OS X) for more entertaining pictures. (http://www.omnigroup.com/omniGraffle)

I usually use the Sigmaplot software for making figures. That is an excellent software.

It looks like everyone has some very good comments on the question. But as you can tell from all of the great answers, the question is not specific, so it can be interpreted in various ways depending on what outcome you are looking for. I would like to add to what David Gärtner shared, and yes, I am biased as this is what I pretend to do for a living at UCDavis. I believe he is "on the mark" with his observation on the types of applications used for this type of work. But nice 3D images can be achieved with programs like Photoshop and Illustrator as well (example attached). I have found over the years that the most successful researchers and scientists that I have had the opportunity to work with will incorporate the cost of having the graphics done into the proposal. This allows for all of their hard work to be represented professionally and be seen in the best light. After all, doesn't all of your hard work deserve it.

Thank you all. I have had closer look at many drawing programs recently. The list includes, Illustrator, Coreldraw, Solidworks, Solidedge (free for students), AutoCAD (free for students), PTC CREO (free for students), Fusion 360 (free for students), Rhino and Cinema 4D. To me, Illustrator and Corel and best for 2D drawings. All others are equally fine for 3D solid modelling. However, I am most impressed by Cinema 4D which is also free for students and is very powerful for making 3D illustrations and animations. True that one needs lot of practice to learn these programs. But I enjoyed it. I believe that a scientist must be able to draw illustrations himself. In this way, we can express or present our thoughts more effectively. A scientist can be a good artist as well. :)

In the early days of software development, programmers used to try to design their own interfaces and art as well. Thus came the derisive term "programmer design", due to the poor results. The industry learned that they had to hire professional designers and artists.

Producing good information graphics requires a lot of training and experience. 3D programs such as Maya take years to master. It's understandable that most of you won't have a budget for a professional artist, but if you are making a proposal you should consider adding that expense. If your school has a graphics program, you might try making an arrangement with them as well.

I have a similar question, I'm not sure if you guys answered it.... all of these software seem great for modeling machines, etc but I need software for modeling biology, for example drawing viral entry into a cell. I'm a pretty good artist as I've been drawing my notes for school since forever but I suck at all computer things. Ideas?

For 2D (and some 3D) graphics my favorite finally was (and is) OmniGraffle (Pro). After experimenting for years with different software, OmniGraffle literally was the killer app for the move to OSX. I haven't tried Visio or similar problems lately, but back in the years of the decision, they were no comparison to OmniGraffle both in the easiness of the user interface and in the professional look of its results (without a hassle the defaults always look good). All of our publications and all illustrations for lecture materials are done with OmniGraffle for more than 7 years.

We have a campus license for Adobe Illustrator hence we can just use it but never do that and stick to OmniGraffle. Of course we have Inkscape but almost never use it. 

For 3D we lately only used good old SketchUp (Pro). Seldomly used the Pro features though. Its even beneficial for animated 3D sketches for videos, which comes in handy for some type of publications besides journals. The competitors we considered included Maya, Cinema 4D, Solidworks, Vectorworks and Blender. Again, the ease of use was the main argument towards SketchUp. We even used it for professional planning of complete houses and blueprints exchanged with professional architects.

here you can find some tips

http://www.keepcalmandpublishpapers.com/

Ebony Nicole Gary,

see my detailed response on page 8 that covers a variety of programs, including some that we develop, for illustrating, modeling, and animating biology from atoms to organisms. It further describes organizations that can teach you techniques of illustration or where you can hire professionals or find collaborators.

So I puttered around with this for a review I'm writing, and made some pretty decent progress using microsoft PowerPoint surprisingly enough. I've used Photoshop before and hated it as it is not at all intuitive, for me (imagine trying to teach a pastry chef to use a fluorescent microscope)! Seems like the best advice is to hire a professional or be lucky enough to have friends in your university's art department!

I prefer Adobe Illustrator It is very simple