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Scientific graphical abstracts — design guidelines

art + design

Math geek? If you like the clean geometric design of the type posters, you may enjoy something even more mathematical. Design that transcends repetition: Art of Pi, Phi and e posters.
Are optotypes your type?
SnellenMK adds lowercase and punctuation to the traditional Snellen design.

Visions of Type

SnellenMK optotype font. Uppercase, lowercase and symbols to test your eyes. (zoom)
SnellenMK optotype font. Uppercase, lowercase and symbols to test your eyes. (zoom)

eyes on the universe

These typographical posters are designed after the style of the Snellen Chart, which is one of the kinds of eye charts used to measure visual acuity.

If you love looking, seeing and the universe, these posters are for you. They are available for purchase.

optotypes

Symbols on such charts are known as optotypes. Fonts by Andrew Howlett exist whose glyphs conform to the properties of optotypes: Snellen font and Sloan font. However, some of the characters in the Snellen font file are a little oddly shaped—I provide my redesign of the Snellen font in which the glyphs are more consistent (see below). Lowercase characters are not available.

For the posters here, I've used either my redesigned Snellen font or Monotype's Rockwell, with minor stroke and kerning adjustments in places. Some symbols, such as on the math chart, were designed by hand.

The numbers on the left side of the posters (e.g. 20/30) are a measure of visual acuity. The numbers on the right provide information about what is shown on the line (e.g. abundance of elements).

Snellen chart design

The charts are designed to be viewed at a distance of 6 meters (20 feet). At this distance, ability to resolve a letter tha subtends 5 minute of arc corersponds to 6/6 (or 20/20) visual acuity. This corresponds to a letter size of $$\frac{2\pi}{360} \times \frac{5}{60} \times 6 = 8.727 \, \text{mm} = 24.74 \, \text{pt}$$

The Snellen optotypes are designed on a 5 × 5 grid and have a fascinating history. For design, Rockwell and Lubalin Graph can be used to approximate Snellen, though these fonts lack the grid structure of the optotypes.

Snellen optotypes are designed on a 5 × 5 grid. At a viewing distance of 6 m (20 ft) each letter on the 6/6 (or 20/20) acuity line must be 8.727 mm (24.47 pt). The optotypes are compared to the characters from the Rockwell Bold font, which is a mediocre approximation. (zoom)

snellen optotype font

My redesign of Andrew Howlett's Snellen optotype font. Read about redesign process—which reinterprets some of the characters and adds lowercase.

Snellen optotypes are designed on a 5 × 5 grid. At a viewing distance of 6 m (20 ft) each letter on the 6/6 (or 20/20) acuity line must be 8.727 mm (24.47 pt) (zoom, zoom, about the design, download Snellen font)

the posters

conventional Snellen charts

These Snellen charts include acuity lines from 20/200 to 20/10.

The charts should be printed at a physical size of 16" × 24" (1150 pt × 1725 pt. At this size, the characters on the 20/20 line subtend 5 minutes of arc when viewed at 6 meters (20 feet), which is the technical specification of the Snellen chart.

When the charts are printed at this size, the two horizontal lines below the 20/30 and 20/20 lines are exactly 8" (576 pt) long. These length markers are my own addition.

If the chart is printed at any other size, the viewing distance changes. To compute the correct viewing distance, $d$, measure the length of these lines, $L$ (in inches) and use $$d = 6 \times L / 8$$

For example, if I print this chart to fit onto an 8.5" × 11" page, these lines are 3.47". Thus, my smaller chart should be viewed from $6 \times 3.47 / 8 = 2.60 \, \text{m}$ (8.53 ft).

Numbers on the left provide visual acuity in feet. Numbers on the right show the denominator of the acuity in feet and its equivalent in meters, rounded to the nearest integer.

The order of the 61 characters on the charts has been limit uniformity and avoid easily perceived patterns—especially in the case of the genetic sequence Snellen. These restrictions (e.g. limit in the number of repeated n-grams) apply across linebreaks.

9 character Snellen

This is the canonical Snellen chart, using the 9 original characters.

$E FP LDO CETD ZOFEL DCZTFP PFLOZDE OZPCELTD TLEFDCOP EDOPTFLC LTCZOEPF FODLPZCT$
1. no more than 8 instances of any character and no fewer than 6
2. no double characters (e.g. PP does not occur)
3. no more than 2 repeats of any 2-gram (e.g. LT ... LT ... LT does not occur)
4. all 3-grams are unique (e.g. LDO does not repeat)
5. no identical adjacent characters across lines within a distance of one positions.
6. for a given line, the characters at the same position in the previous 6 lines are all different.
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A technically accurate Snellen chart using traditional 9 characters C D E F L O P T Z rendered as optotypes. Print at 16 in × 24 in. ( BUY ARTWORK )

26 character Snellen

This chart uses all the letters of the alphabet and is typset using my Snellen font redesign.

1. all letters of the alphabet are used
2. no more than 3 instances of any character
3. no double characters (e.g. PP does not occur)
4. all n-grams (n = 2, 3, ...) are unique
5. on a given line, all characters are unique
6. no identical adjacent characters across lines within a distance of 8 positions.
7. for a given line, the characters at the same position in all other lines are all different.
$E FP NBJ GCHQ RKVNX PZLSAY IMEXDBU CYRAVQGH LWKPIJZO XUBHRFEV JTDIGSYZ QFWLMUKA$
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A technically accurate Snellen chart using all 26 letters of the alphabet rendered as optotypes. All n-grams are unique. Print at 16 in × 24 in. ( BUY ARTWORK )

genomic sequence Snellen

Since I work in a genome center, the one below is the one we'd use. Thanks to Dr. Nüket Bilgen for suggesting that the chart start with ATG (start codon) and end with one of the stop codons (TAG, TGA, but not TAA since no two adjoining characters can be the same).

1. no more than 19 instances of any character and no fewer than 15
2. no double characters (e.g. AA does not occur)
3. no more than 7 repeats of any 2-gram
4. no more than 4 repeats of any 3-gram
5. no more than 2 repeats of any 4-gram or 5-gram
6. for a given line, the characters at the same position in the previous 2 lines are different
7. chart starts with start codon ATG
8. chart ends with stop codon TAG, which appears only once; the other two stop codons (TGA, TAA) do not appear on the chart
$A TG CAT ATCG GCATA CGTCTG TACAGAC GTGTACGA CGAGCTAT ACTCTGTG GTCAGAGC CGAGATAG$
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A technically accurate Snellen chart using four genetic bases A T G C rendered as optotypes. The chart begins with the start codon ATG and ends in the stop codon TGA, which appears only once in the chart. Print at 16 in × 24 in. ( BUY ARTWORK )

The best alignments of this chart's sequence are to fungus (Leptosphaeria maculans lepidii, 35/42, 83%) and a tapeworm (Diphyllobothrium latum, 24/26, 92%). Thanks to Lorraine May for this observation!

nautical flags Snellen

Charts ahoy!

$Z KE CHG XVRM YTWUS JQFINB EZAOXLD NHKVCUGF SWRMIAZP DBTOJYXE FZHLNUKA IVGMYCWR$
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A technically accurate Snellen chart using the nautical flag alphabet rendered as optotypes. Print at 16 in × 24 in. ( BUY ARTWORK )

The flag alphabet has been designed to match, as closely as possible, to the style of the Snellen optotypes. In some cases this required that the geometry of the flag had to be adjusted—this may upset the purists and cause havoc on the waterways.

Proportions of colors has been adjusted in some flags to fit symmetrically into the 5 × 5 optotype grid. The checker of N is now a 5 × 5 grid. The number of stripes in Y has been reduced—the width of each stripe is now 20% of the width of the flag. Proportions in C, D, J, R, S, T, W and X have been adjusted so that color strips are a multiple of 20% of the width of the flag. The cross in M and V matches the X used in the Snellen font.

Snellen optotypes for the nautical flag alphabet. (zoom)

eyes on the elements

Elements are sorted in order of abundance. The numbers on the left show the max and min $-log_{10}$ abundance of the elements listed on a given line. For example, 3.0/3.3 for the "N Si Mg S" line in the abundance of elements in the universe indicates that abundance of N is 0.001 and of S is 0.0005.

You can download my tidy plain-text table of abundance of elements in the universe (original source, 83 elements) and table of abundance of elements in the body (original source, 60 elements). These have been parsed from the original sources and give the $-log_{10}$ abundance for various elements.

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Snellen Chart of abundance of the elements in the universe. ( BUY ARTWORK )
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Snellen Chart of abundance of the elements in the human body. ( BUY ARTWORK )

eyes on physical constants

44 of the most interesting physical constants ranging from the very large (Planck temperature $T_p = 1.4 \times 10^{32} \mathrm{K}$) to the very small (cosmological constant $\Lambda = 1.19 \times 10^{-52} \mathrm{m}^{-2}$). You can download the table of constants and their values.

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Snellen Chart of physical constants. ( BUY ARTWORK )

eyes on mathematical symbols

44 intriguing and perhaps mysterious mathematical symbols ranging from common equality $=$ to the esoteric normal subgroup $\triangleleft$.

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Snellen Chart of mathematical operators and symbols. ( BUY ARTWORK )

where's the chart?

The chart is the visual form of a rhetorical question. The letter layout here is the same as in the canonical Snellen chart, which is limited to the 10 Sloan letters C, D, E, F, L, N, O, P, T, Z.

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Snellen Chart typeset in Braille. ( BUY ARTWORK )
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Snellen Chart typeset in Braille. Variant #2. ( BUY ARTWORK )
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Snellen Chart typeset in Braille. Variant #3. ( BUY ARTWORK )

Music for the Moon: Flunk's 'Down Here / Moon Above'

Sat 29-05-2021

The Sanctuary Project is a Lunar vault of science and art. It includes two fully sequenced human genomes, sequenced and assembled by us at Canada's Michael Smith Genome Sciences Centre.

The first disc includes a song composed by Flunk for the (eventual) trip to the Moon.

But how do you send sound to space? I describe the inspiration, process and art behind the work.

The song 'Down Here / Moon Above' from Flunk's new album History of Everything Ever is our song for space. It appears on the Sanctuary genome discs, which aim to send two fully sequenced human genomes to the Moon. (more)

Happy 2021 $\pi$ Day—A forest of digits

Sun 14-03-2021

Celebrate $\pi$ Day (March 14th) and finally see the digits through the forest.

The 26th tree in the digit forest of $\pi$. Why is there a flower on the ground?. (details)

This year is full of botanical whimsy. A Lindenmayer system forest – deterministic but always changing. Feel free to stop and pick the flowers from the ground.

The first 46 digits of $\pi$ in 8 trees. There are so many more. (details)

And things can get crazy in the forest.

A forest of the digits of '\pi$, by ecosystem. (details) Check out art from previous years: 2013$\pi$Day and 2014$\pi$Day, 2015$\pi$Day, 2016$\pi$Day, 2017$\pi$Day, 2018$\pi$Day and 2019$\pi` Day.

Testing for rare conditions

Sun 30-05-2021

All that glitters is not gold. —W. Shakespeare

The sensitivity and specificity of a test do not necessarily correspond to its error rate. This becomes critically important when testing for a rare condition — a test with 99% sensitivity and specificity has an even chance of being wrong when the condition prevalence is 1%.

We discuss the positive predictive value (PPV) and how practices such as screen can increase it.

Nature Methods Points of Significance column: Testing for rare conditions. (read)

Altman, N. & Krzywinski, M. (2021) Points of significance: Testing for rare conditions. Nature Methods 18:224–225.

Standardization fallacy

Tue 09-02-2021

We demand rigidly defined areas of doubt and uncertainty! —D. Adams

A popular notion about experiments is that it's good to keep variability in subjects low to limit the influence of confounding factors. This is called standardization.

Unfortunately, although standardization increases power, it can induce unrealistically low variability and lead to results that do not generalize to the population of interest. And, in fact, may be irreproducible.

Nature Methods Points of Significance column: Standardization fallacy. (read)

Not paying attention to these details and thinking (or hoping) that standardization is always good is the "standardization fallacy". In this column, we look at how standardization can be balanced with heterogenization to avoid this thorny issue.

Voelkl, B., Würbel, H., Krzywinski, M. & Altman, N. (2021) Points of significance: Standardization fallacy. Nature Methods 18:5–6.

Graphical Abstract Design Guidelines

Fri 13-11-2020

Clear, concise, legible and compelling.

Making a scientific graphical abstract? Refer to my practical design guidelines and redesign examples to improve organization, design and clarity of your graphical abstracts.

Graphical Abstract Design Guidelines — Clear, concise, legible and compelling.