Slashdot Mirror
Graphics in Science
BishopBerkeley writes "Nature has an interesting nugget about the second meeting of the Image and Meaning Initiative which was held at the Getty Museum in Los Angeles. It is about the use of graphics in presenting scientific data. I am also a big advocate of using nice graphics in scientific presentations, but I also agree with Felice Franel, the founder of I-M, that not all images are meaningful scientifically. In fact, one encounters (and I am ashamed to admit that I have published) images that look nice but have no scientific import at all. One very cool Harvard physics professor, Eric Heller, produces wickedly beautiful (and meaningful) images of quantum mechanical models. These images have made the covers of Science and Nature, and are featured in his online art gallery, which was reviewed in the New York Times in 2002." And of course, any mention of graphic information should not go by without a big shout out to Edward Tufte.
Nature has symmetry everywhere. GUT of science and art.
"In fact, one encounters (and I am ashamed to admit that I have published) images that look nice but have no scientific import at all."
Fianlly, an excuse to buy that 7800 GTX!
I know how they make these: it's with this!
I've struggled with the same question as a computer consultant -- do images always convey anything useful just because they are based on scientific data? I've created a lot of really cool graphs and 3-D animations, but as far as analyzing the data, most times the computer is a lot better at processing multi-dimensional data than our old Mark-1 eyeball.
But there is a cool factor involved with a lot of imaging. You can't deny that.
Probably more disturbing is when images appear to convey data when they really don't. The use of false color is a great tool to bring out detail in astonomical images, but many times is misleading to the casual observer who may not understand that the images are "doped"
Is BitTorrent Next?
> not all images are meaningful scientifically. In fact, one encounters [...] images that look nice but have no scientific import at all
Could you show that with a diagram or something?
Sheesh, evil *and* a jerk. -- Jade
Sometimes, it is easier to demonstrate with graphics, but a powerpoint presentation (or OOo presentation) with only a few words is not good either when demonstrating to more than a few people. Your information should be represented in many ways (graphical, text) because individuals learn things differently.
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Here are the mirrordot links:
Nature has an interesting nugget
Image and Meaning Initiative
Eric Heller
online art gallery
New York Times
shout out to Edward Tufte
j0b.org - A famous domain name for sale
Your are right. Most of the time NASA is not even concerned about color photographs. They usually focus on the wavelengths we can't see. In some of their missions the camera was not even color balanced correctly. You can tell because the American flag seen in some pictures is a really funky color. It's annoying when a space agency can not even get the color of a planet correctly.
The Design Museum in London has a whole section devoted to the presentation of information and the way bias can be introduced depending on the method selected.
They have everything from pie-charts prepared by Florence Nightingale comparing the death rates in battle vs. the field hospitals to a graphical representation of the Linux Kernel.
Well worth a look.
Why does this tufte guy get so much credit for so little, much of whih is either wrong or opinions on design, which, by definition, are subjective matters.
once we stop kow towing to the tuftewrongs, we might get somewhere.
In Soviet Russia scientific data presents powerpoint.
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What is your favourite open source cross-platform toolkit for making scientific graphs?
10 ?"Hello World" life was simple then
not the other way around.
If you put your entire presentation in your slides, then there is no need to listen to you.
My apologies if this was not your intent with this statement, but I have seen quite a few presentations where the person presenting really had no need to be there because the whole thing was in the PowerPoint slides. IMHO, this is bad presentation style.
"Empathise with stupidity, and you're halfway to thinking like an idiot." - Iain M. Banks
I am about to start a course in Computation Biology and bought Fundamentals of Biochemistry (Voet) as some background reading. The maths leaves me cold and when an equation is rearranged I just can't grasp the significance of it.
However, the graphics of 3D molecular structures that start off simple and then end up in a huge DNA helix just blow me away and I spent yesterday morning staring at them in wonder (more than I have ever studied a work of art). Somebody put a lot of effort into that and I now have an appreciation and wonder of the mechanisms of life.
This reminds me of this issue:
Slate explains that the raw images from space telescopes are colored with Photoshop before they are released to the public. The 'Pillars of Creation' shows the difference that color makes. You can download the free Photoshop plug-in to color your own images.
I have long lamented the lack of visual effort in interface design, specifically in the realm in which I currently work, musical synthesizers.
.. and I have concluded that one of the reasons we see waves of synth revivial occurring every few years is because that is how long it takes someone to 'grok' their synthesizer, and while we wait for that grok to occur, no use occurs.
One of the problems with synthesis today is that it is too scientific
I recently made a commitment as a synth builder to attempt to enforce a few rules on myself; one of them is the "No Label Philosophy", which basically means that if a knob needs a label in order for the user to work out what it does when they turn it, then its a poor interface design, but if it doesn't, its a strong one.
The question I have is, where are other examples of 'illustration pushing concept' in the slashdott'ers world today? Have you recently seen some examples of graphical/icon-based design being used to clearly communicate very high-order concepts to the end user? What are they? Anyone got any pointers to examples of superlative graphical interface function, where you know instinctively what is going to happen because the picture tells you so?
; -- the corruption of government starts with its secrets. a truly free people keep no secrets. --
The problem is most felt in dealing with non-specialists. For example, all microscopists will instantly recognize the implications of a given visual patterns of an osmium tetroxide stain in an image. In contrast, other scientists, lay people, voters, politicians, PHBs, etc. need some grounding in what the image shows, how it differs from "normal" and what the image means. A few suggestions for improving the understandability of an image include:
- textual summary: text creates reinforcement/redundancy
- annotate the images: arrows, circled regions and call-outs help the viewer know what's important and what it is.
- legends: color images, especially, need a legend or textual explanation of the color scheme.
- supporting metadata: information such as subject, scale, time (relative to some event), etc. helps create meaningful context.
- contrasting image pairs: Image pairs or sequences help cue viewers to the significant features or establish a pattern. Showing before & after, normal vs. abnormal, enhanced vs. non-enhanced, overview vs. detail, plain vs. peanut, etc. helps explain what's what.
A picture may be worth a thousand words, but if an image presenter wants the viewer to get the intended thousand words then a little extra annotation, metadata, and context can help.Two wrongs don't make a right, but three lefts do.
I prefer an image or an example to an obscure equation. Some scientists like to show that they are "hot" by publishing long lists of equations even those in the field find hard to decypher. It is better to understand through examples than not to understand at all.
proxi
I am a master's student in the geo-sciences and my thesis requires that i process and handle a tremendous amount of data
Most of the data that i use is spatial: topography, bathymetry, salinity concentrations..
Anyway, my point is that after i write some code to process the data
(I am developing an ecological model that tracks subsidence of marshland based on a whole bunch of environmental and geophysical parameters)
the best and easiest way for me to verify the output is reasonable is to draw a picture of it. I have spent probably 60% of my time writing software that displays the data in a graphical format.
However, this is only to verify that my data is close to accurate.. like say everything looks like it should.
You still can't beat some statistics for really checking the quality of the output.
Also, after watching a large number of presentations on theses, scientific studies, etc.. i would say that 0.05% of those presenters know nothing more of scientifc graphing than pushing buttons in xcel and seeing the nice graphics that pop up.
I mean, most of them dont even change the default graphic colors, so they are up there, talking about something and behind them is that crappy Xcel purple color.
Another example of scientific art is this very beautiful animation of some sort of fractal. (Note: Turn down sound volume prior to viewing.)
I think therefore I am. Therefore, I think, I am.
It would be a shame if journal article authors never looked past the default MS Excel graphs for their presentation.
i personally prefer opendx for my scientific data, it's somewhat complex but can make great navegable visualizations.
Import has the connotations of weight and substance. Importance is a higher, lighter word, more filled with urgency and less with long-term consquences.
Import is conventionally associated with the adjective "dire," and is more recognizable in that context.
"The coughing of the villagers was filled with dire import."
There's a sort of feeling that "import" is a substance there which is almost too intense for modern language. "Import" is also often associated with the verb "fraught." This heaviness is probably because import, as a noun, is closer to the import as a verb. There's more activity left over.
Because of these connotations, importance is not a reasonable replacement for import in all cases. It's a modified and weaker version of the word, as suffixed variations often are.
All this is to say demonstrate that while the point of the article is certainly user comprehension, those of us with 19th century literary educations don't even notice a word like that is archaic. We assume it's still in common parlance because the sources from which we initially gleaned it are very nearly modern in their syntax. There's just no way to reliably expunge a broad vocabulary of archaic usages.
In my experience in science keeping graphics very simple is best. I usually hope to have the audience leave my presentations with three adjectives in mind when they critique it: simple, clean, and creative. Assuming that you have followed rules of grammar and your scientific method is sound, a simple yet innovative presentation can make a good memory. Your data will be well understood and remembered. I absolutely detest the obligatory sequence data slide that creeps into many science presentations. Surely a creative scientist will someday discover a better way to effectively communicate sequence data in a presentation. And, how many people are going to stand at your poster for 4 hours to hand-copy all of your sequence data?
This page: http://www.jimworthey.com/jimtalk2004nov.html is the graphics that I used for a talk last year. As you read through, you'll see 3D pictures and animated graphics. When you see a 3D graph with a border, that links to a VRML pic that you can zoom and rotate. For free VRML viewer see http://www.parallelgraphics.com/ for example.
I'm the author of an easy to use open source C++ library that helps bridge the gap between your science and a final high quality image, and I thought I might point it out, since it's relevant to the topic.
PNGwriter was originally written with scientists in mind. The need to create an image from the result of a scientific computer simulation arises as a natural part of scientific programming. Getting the data out of the program and into a high quality image in an efficient way can sometimes be hard, especially if the user is not a very experienced programmer. The methods used can often be highly inefficient or too complex to be feasible.
PNGwriter is a very easy to use open source graphics library that uses PNG as its output format. The interface has been designed to be as simple and intuitive as possible. It supports plotting and reading in the RGB (red, green, blue), HSV (hue, saturation, value/brightness) and CMYK (cyan, magenta, yellow, black) colour spaces, basic shapes, scaling, bilinear interpolation, full TrueType antialiased and rotated text support, bezier curves, opening existing PNG images and more. Documentation in English and Spanish. Runs under Linux, Unix, Mac OS X and Windows. Requires libpng and optionally FreeType2 for the text support.
It has been packaged for or is a part of Debian (stable), Ubuntu, Arch and FreeBSD.
The website is available in English, Spanish and (in summary form) in Japanese, and contains many examples, an online version of the PDF manual, a FAQ section and more.
Take a look:
http://pngwriter.sourceforge.net/
Hope you find it useful!
My motorbike travels in Chile.
Once upon a time..
(A fairytale of magic pictures)
--
"A kind of HTML, the codingsystem used for the layout of webpages, but
then for graphics". That's what SVG is about. SVG is an abbreviation of
Scalable Vector Graphics and describes how something is to be presented.
The thickness of the lines, the patterns to fill planes, color
distribution, masks and filters for effects like smooth flows, and more.
In August of this year a international conference on SVG is held in
Enschede and Ruud Steltenpool# is one of the organisers. In this edition
of OpenMagazine he tells, mostly by using a fairytale, what makes SVG so
interesting.
--
by Ruud Steltenpool
The little girl open*s the 'story-book' (2 screens fit together as pages
with a computer and a wireless connection integrated) and sees a young
lady, a princess of course, standing next to a pond, her face *the same
as* as the girl's own.
"Shall i tell you a story?", asks the princess and the kid silently
mumbles "yes, pwease".
"Once upon a time..." starts the princess and unfolds the story while the
words appear one by one on the other page. The drawings change along
accordingly, not really continuously moving images, but more like a
richly illustrated book. When the little girl touches the dwarf picture
in front of her, the princess departs slightly from her story and tells
about the dwarf, who in turn also makes himself heard. Yesterday the
dwarf was a
unicorn and tomorrow a magical bird maybe, cause the story changes based
on interaction with the girl. Stories can get saved - "same as yesterday"
says the girl - or it can be a never ending story growing with the child.
Maybe in interaction with the stories of hundreds of thousands of other
children.
"Scalable Vector Graphics" is the quite imposing term for these pictures,
the words and the connections. A bit of technical speach, that next to the
obvious, carries along lots of extra meaning. Many people that work with
it, therefore rather use the abbreviation SVG, because the full variant
sells it short. A better description of this technology might be 'magical
pictures'.
Pixels
An ordinary picture in a page is usually far from magical, whether it's a
local document or on a webpage or whatever. Apart from maybe the place and
size in the page, they contain no information about themselves. Of course
you can make such an ordinary picture clickable (link it), maybe even
make the result dependent on where you click and add a short description
in HTML that might serve as a pop-up text. This however changes nothing
to the fact that the picture is just a bunch of colored pixels, without
any built-in meaning. No semantics, as its called in computerlingo.
Now imagine you do are able to put this meaning in. So every element in
the image - the princess, the pond, the dwarf, maybe even the horn of the
unicorn - would hold enough information to identify itself. Or enough
information to change the representation of itself or its surrounding,
for example by moving, turning, growing, shrinking or changing the
colors. Also imagine that this image can communicate with the internet,
save information about itself, renew stories, maybe communicating with
other stories so in case of common story lines one could start a joined
adventure. It are all possibilities of SVG.
SVG in essence is a language that describes images in text. It describes
how something must be presented: the thickness of the lines, the patterns
to fill the planes, color distribution, masks and filters for subtle
effects. And more. So only at the final moment of presenting this
description is calculated into pixels. Also it can flourish images into
animations: movements along complicated paths, a poisoned apple fluently
going from sickly purple to tempting red, or the girl that grows after
drinking from the bottle saying "Drink me". SVG controls the flow of text
Why does this tufte guy get so much credit for so little, much of whih is either wrong or opinions on design, which, by definition, are subjective matters.
Judging from the spelling in your post, I'm guessing this is a troll but I'll bite anyhow. One of Tufte's messages is to maximize the data-ink ratio. One way of doing that is by doing "so little" as you put it. Many of the standard plot styles (e.g., bar chart) and be redesigned slightly by removing extraneous graphical elements to make the data really stand out. So doing "so little" is an advantage. Note that it takes a lot of thought to do "so little" so implying that anyone can do it is just plain wrong.
Part of the reason I am wasting time replying to this troll is because I wanted to tell slashdot readers that if they have an interest in Tufte or this type of material that I would strongly encourage you to go to one of his seminars. I was fortunate enough to see one and it was worth every penny ($320 and that includes the price of his three books, that PowerPoint pamphlet, and the famous Napolean march poster). I was scribbling notes as fast as I could for most of the day. He will give you a very good overview of the material he covers in his books. For example, he starts off the day stating about 10-12 key principles of information design. The principles are never really listed in any of his books. They are all covered, of course, but having him rattle them off -- with examples of each -- was worth the cost right there.
I'm not one to recommend seminars and conferences. If you ask me, they are oftentimes just an excuse to get the company to pay for a semi-vacation from the office. People ought to stay in their fucking offices and get some god damn work done. But this Tufte course is a rare exception. Again, I strongly recommend taking his course if he comes to your area.
GMD
watch this
Edward Tufte hosts Pimp My Graphic.
The Web would be a lot better if a webmaster could implicitly mirror a remote page that's linked a page on their home server. I could add a link through a caching proxy, send a notice to the remote webmaster. The proxy could periodically send copies of its transaction log to the remote webmaster. Dropping the proxy from the loop, or just falloff of traffic through my link to zero, would stop the transmission of log info.
All those steps could be automated. Perhaps an Apache module that lets an admin specify a link through a Web interface, which sets a rewrite rule to rewrite cached links in sent pages, is the right package. The module rewrites the link, to instead point at the caching proxy, sends the proxy the message to notify the original server, and emails the original server's webmaster.
--
make install -not war
Graphics help us understand because they make use of a big part of our wetware, the visual cortex. Instead of leaving all those neurons idle, an image engages them to coprocess, helping us "get it" faster. "Oh, now I see!"
I will be happy as soon as they stop showing black holes and wormholes as being fucking funnels. Every Sci-fi or news show displays them as a funnel, when everyone who knows about them, knows that they are spheres. I know the producers don't care but why can't the shows science advisors put their foot down for once.
As a programmer and sometimes teaching assistant I've been doing a lot of stuff with techniques to represent the structure of information (ER models, UML class diagrams, RDF, etc.) and of discrete processes (state machines, flow diagrams, Petri nets, UML activity diagrams, UML message sequence charts, etc.)
Considering the popularity of such techniques I find it odd how little material I have encountered on their actual useability, compared to other forms of representation. There still appear to be hordes of professionals in the software industry who routinely dismiss diagram techniques as being useless, or worse, a tell-tale sign of a weak mind (as Dijkstra did), without feeling the slightest need to substantiate such sentiment with evidence of any kind. At the same time, none of the proponents of diagram techniques I have seen (speaking or in writing) make any serious useability arguments in favour. Clearly it's easy to draw up small examples on which a particular diagram technique does well, and other examples to discredit the same technique. But that is the full extent to which the matter seems to be dealt with, even among professional software design specialists, such as the designers of the UML.
So what I have been reading, mostly between the lines, is that formulas are "too hard" while diagrams are "too easy". Well, on the whole there may be a grain of truth in this thought, but I'd like to see more details. Are there any serious studies on the useability for diagrams (vs. that of tables, or formulas, or other types of visualizations) for conveying information? Or is this whole subject really as trivial as everybody appears to believe?
As an astronomer/physicist, I have to vote for http://www.astro.princeton.edu/~rhl/sm/, which produces graphs which just look much nicer than anything gnuplot or Matlab will spit out (with similar sort of effort, although maybe SM has a slightly weirder scripting language). Not free or open source, but it is, uh, obtainable, if you know what I mean.
The world is everything that is the case
I know what they're talking about. Quite a few times I have seen a very nice graphic of HIV infecting a cell or whatever, only to realise the DNA helix is going the wrong way.
The best tool for sharing the graphics after they are produced is http://depicto.com/
Depicto is great. It lets you and other remote users interactively comment/edit/modify graphics. One of the best remote-office tools I've seen in a while.
Disclaimer: I don't have any stake in Depicto but I am friends with the developer.
Space and Computers.
Incidentally, the summary gets the name wrong. It's not Felice Franel, but Felice Frankel.
to create graphics out of scientific output is to close the cycle - hence, any data that can be gained from the graphic can not be inputted back into a computer for processing... and anything that a human can get out of a graphic is just a boost of imagination - there is no solid data in a graphic (our brain works to tie data and a graphic together) so why can't u just work with solid data?
> extracting information in those other designs.
No, you can't.
How do I know that? Because you foolishly leaped to say the opposite of a very simple and non-controversial statement. Let's take a look at it:
You can easily do experiments that show that viewers have an easier time extracting information in a specific graphic design than in others.
Let's have one graphic design in the experiment be a standard set of histograms. Let's let the other graphic design be the same histograms, with 200,000 other random histograms jammed in there for no reason.
I can guarantee you that no viewers will have an easier time extracting information from the latter design than from the former. Hence, your kneejerk "well, I can do the opposite, so nyah!" claim is just nonsense.
There are useful observations to be made about different viewers and different graphic designs, but it'll take a lot more thought than you put into that one.