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art + design
VISIONS OF TYPE | Put my typographical posters on your wall. (buy artwork / see all my art)
Support Ellie Balk's Kickstarter community math mural project in which Brooklyn students learn math and art to visualize π.
My SnellenMK font adds lowercase and punctuation to the traditional Snellen design.

# Visions of Type

SNELLEN CHARTS | A collection of classic and modern charts. (buy artwork / see all my art)

## 1 · a font to test your eyes

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.

## 2 · 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).

## 3 · 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)

## 4 · snellen optotype font

SNELLENMK FONT | A complete Snellen type face with upper- and lowercase. (buy artwork / see all my art)

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)

## 5 · classic and modern eyechart posters

SNELLENMK FONT | Look! (buy artwork / see all my art)

### 5.1 · conventional eye charts

THE CANONICAL 9-CHARACTER SNELLEN CHART | This classic chart uses 9 letters: C D E F L O P T Z. (buy artwork / see all my art)

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.

#### 5.1.1 · 9-character eye chart

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.
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)

#### 5.1.2 · 26-character eye chart

THE EXPANDED SNELLEN CHART | This chart uses my Snellen optotype font and uses all 26 letters. (buy artwork / see all my art)

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.
$E FP NBJ GCHQ RKVNX PZLSAY IMEXDBU CYRAVQGH LWKPIJZO XUBHRFEV JTDIGSYZ QFWLMUKA$
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)

#### 5.1.3 · sorted alphabet eye chart

THE SNELLEN CHART | This chart uses my Snellen optotype font and shows its letters in sorted order. (buy artwork / see all my art)

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

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)

### 5.2 · genomic sequence eye chart

THE GENOMIC SNELLEN CHART | Sequencing, by eye. (buy artwork / see all my art)

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
$A TG CAT ATCG GCATA CGTCTG TACAGAC GTGTACGA CGAGCTAT ACTCTGTG GTCAGAGC CGAGATAG$
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!

### 5.3 · nautical flag eye chart

THE MARITIME SNELLEN CHART | Charts ahoy! (buy artwork / see all my art)

Charts ahoy!

$Z KE CHG XVRM YTWUS JQFINB EZAOXLD NHKVCUGF SWRMIAZP DBTOJYXE FZHLNUKA IVGMYCWR$
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)

### 5.4 · eyes on the elements — chemical eye charts

THE CHEMICAL SNELLEN CHART | Elements, ordered either by abundance in the universe (H, He, O, ...) or in the human body (O, C, H, ...). (buy artwork / see all my art)

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.

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

### 5.5 · physical constants eye chart

THE PHYSICS SNELLEN CHART | A collection of intersting physical constants, sorted from the very large to the very small. (buy artwork / see all my art)

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.

Snellen Chart of physical constants. (BUY ARTWORK)

### 5.6 · mathematical symbol eye chart

THE MATH SNELLEN CHART | Operate this! (buy artwork / see all my art)

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

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

### 5.7 · where's the chart — braille eye charts

THE INVISIBLE SNELLEN CHART | Can you feel it? (buy artwork / see all my art)

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.

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

# Neural network primer

Mon 06-02-2023

Nature is often hidden, sometimes overcome, seldom extinguished. —Francis Bacon

In the first of a series of columns about neural networks, we introduce them with an intuitive approach that draws from our discussion about logistic regression.

Nature Methods Points of Significance column: Neural network primer. (read)

Simple neural networks are just a chain of linear regressions. And, although neural network models can get very complicated, their essence can be understood in terms of relatively basic principles.

We show how neural network components (neurons) can be arranged in the network and discuss the ideas of hidden layers. Using a simple data set we show how even a 3-neuron neural network can already model relatively complicated data patterns.

Derry, A., Krzywinski, M & Altman, N. (2023) Points of significance: Neural network primer. Nature Methods 20.

Lever, J., Krzywinski, M. & Altman, N. (2016) Points of significance: Logistic regression. Nature Methods 13:541–542.

# Cell Genomics cover

Mon 16-01-2023

Our cover on the 11 January 2023 Cell Genomics issue depicts the process of determining the parent-of-origin using differential methylation of alleles at imprinted regions (iDMRs) is imagined as a circuit.

Designed in collaboration with with Carlos Urzua.

Our Cell Genomics cover depicts parent-of-origin assignment as a circuit (volume 3, issue 1, 11 January 2023). (more)

Akbari, V. et al. Parent-of-origin detection and chromosome-scale haplotyping using long-read DNA methylation sequencing and Strand-seq (2023) Cell Genomics 3(1).

Browse my gallery of cover designs.

A catalogue of my journal and magazine cover designs. (more)

Thu 05-01-2023

My cover design on the 6 January 2023 Science Advances issue depicts DNA sequencing read translation in high-dimensional space. The image showss 672 bases of sequencing barcodes generated by three different single-cell RNA sequencing platforms were encoded as oriented triangles on the faces of three 7-dimensional cubes.

My Science Advances cover that encodes sequence onto hypercubes (volume 9, issue 1, 6 January 2023). (more)

Kijima, Y. et al. A universal sequencing read interpreter (2023) Science Advances 9

Browse my gallery of cover designs.

A catalogue of my journal and magazine cover designs. (more)

# Regression modeling of time-to-event data with censoring

Mon 21-11-2022

If you sit on the sofa for your entire life, you’re running a higher risk of getting heart disease and cancer. —Alex Honnold, American rock climber

In a follow-up to our Survival analysis — time-to-event data and censoring article, we look at how regression can be used to account for additional risk factors in survival analysis.

We explore accelerated failure time regression (AFTR) and the Cox Proportional Hazards model (Cox PH).

Nature Methods Points of Significance column: Regression modeling of time-to-event data with censoring. (read)

Dey, T., Lipsitz, S.R., Cooper, Z., Trinh, Q., Krzywinski, M & Altman, N. (2022) Points of significance: Regression modeling of time-to-event data with censoring. Nature Methods 19.

# Music video for Max Cooper's Ascent

Tue 25-10-2022

My 5-dimensional animation sets the visual stage for Max Cooper's Ascent from the album Unspoken Words. I have previously collaborated with Max on telling a story about infinity for his Yearning for the Infinite album.

I provide a walkthrough the video, describe the animation system I created to generate the frames, and show you all the keyframes

Frame 4897 from the music video of Max Cooper's Asent.

The video recently premiered on YouTube.

Renders of the full scene are available as NFTs.