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In Silico Flurries: Computing a world of snow. Scientific American. 23 December 2017


Fonts + Design

Snellen Optotype Font with Upper and Lowercase characters

In the process of designing my Snellen Eye Chart typographical posters, I came across the Snellen font by Andrew Howlett. I wasn't happy with all the letters, so I made attempts at giving the font an update.

Not being a font designer, I will likely get myself into trouble.

snellen chart posters

While making my Snellen chart series, I entered the rabbit hole of optotype fonts ... and I can't get out!


Typographical posters of how the world works in the style of Snellen eye charts
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca buy artwork
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)

Typographical posters of how the world works in the style of Snellen eye charts
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca buy artwork
A technically accurate Snellen chart using the nautical flag alphabet rendered as optotypes. Print at 16 in × 24 in. (BUY ARTWORK)

The charts don't necessarily use the latest version of my Snellen font design, which fluctuates as my mood about some of the letters changes.

optotype fonts

The optotype requirement is that letters be designed on a 5 × 5 grid, and have constant stroke width. This means that both lower and upper case letters need to share the grid and stroke. To stay compatible with the eyechart paradigm, letters should be as obvious as possible.

Lorrie Frear's article What are Optotypes? Eye Charts in Focus is a great read about optotypes and eye charts.

Snellen Optotype Letter Design

uppercase

The uppercase letter design uses Herman Snellen's original chart as inspiration.

I have modified the design by Andrew Howlett (see below) for some letters. All the changes are relatively minor: more serifs and consistent stroke width for bars on R and K.

lowercase

The lowercase characters should be considered experimental.

The progress of my redesign is shown below. I would greatly appreciate feedback and suggestions!

Download Snellen Optotype Font

The distribution contains both Andrew's version and my redesign.

v7.1 4-jun-2018 — Download Snellen optotype font

version 7.1 — 4 Jun 2017

Tidied all letter forms with Fontlab 6.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Snellen optotype font (version v7.1 4-jun-2018) that includes both upper and lower case characters, along with most punctuation and some symbols. Based on design by Andrew Howlett. (zoom, download Snellen optotype font)

version 7 — 6 Feb 2017

Fixed g and e. Thanks to Makeesha Fisher for suggestions.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Snellen optotype font (mk.v.7). Original design by Andrew Howlett (left) and my redesign (right), which includes both upper and lowercase letters as well as digits and symbols. (zoom, download Snellen optotype font)

version 6 — 5 Feb 2017

Adjusted serifs on f, j, l, o, t to extend the full width of the grid. Added a lot more symbols.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Snellen optotype font (mk.v.6). Original design by Andrew Howlett (left) and my redesign (right), which includes both upper and lowercase letters as well as digits and symbols. (zoom, download Snellen optotype font)

version 5 — 4 Feb 2017

Added lowercase, digits and symbols.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Snellen optotype font (mk.v.5). Original design by Andrew Howlett (left) and my redesign (right), which includes both upper and lowercase letters as well as digits and symbols. (zoom, download Snellen optotype font)

version 4 — 23 Feb 2017

Adding digits.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Snellen optotype font (mk.v.4). Original design by Andrew Howlett (left) and my redesign (right), which includes both upper and lowercase letters as well as digits. (zoom)

version 3 — 22 Feb 2017

I'm exploring the lowercase characters. I don't know what I want to do with them. Make this into a more standard font in which lowercase letters are smaller, so that letters can fit their roles clearly when text is set in sentence case, or fill out the full optotype grid.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Snellen optotype font (mk.v.3). Original design by Andrew Howlett (left) and my redesign (right), which includes both upper and lowercase letters. (zoom)

version 2 — 22 Feb 2017

Flushed out some inconsistencies in the uppercase characters. Added serifs to more letters.

Now all the letters occuppy the full 5 × 5 grid, including the I, whose serifs were widened to allow this. While this new uppercase I isn't as pretty as the old one, it makes the entire typeface more consistent to its optotype roots.

Still struggling with the G. In the original version, the descending stroke was cut off in the middle of a grid, which I didn't like.

The S has been fixed—thanks to Elanor Lutz for feedback.

I've color coded the characters slightly differently, drawing attention to ones that I feel need more thought.

The lowercase characters aren't color coded (yet) because ... most of them need help. Primarily, I'm vacillating between making them fill the full size of the 5 × 5 square, just like the uppercase characters, and keeping them confined to a 4 × 4 square, which incurs loss of legibility. If I make the letters the same size, it will be impossible to distinguish lowercase and uppercase characters some cases (e.g. c, i). Perhaps this is desired?

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Snellen optotype font (mk.v.2). Original design by Andrew Howlett (left) and my redesign (right), which includes both upper and lowercase letters. (zoom)

version 1 — 22 Feb 2017

First attempt at lowercase characters.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Snellen optotype font (mk.v.1). Original design by Andrew Howlett (left) and my redesign (right), which includes both upper and lowercase letters. (zoom, download font)
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news + thoughts

Predicting with confidence and tolerance

Wed 07-11-2018
I abhor averages. I like the individual case. —J.D. Brandeis.

We focus on the important distinction between confidence intervals, typically used to express uncertainty of a sampling statistic such as the mean and, prediction and tolerance intervals, used to make statements about the next value to be drawn from the population.

Confidence intervals provide coverage of a single point—the population mean—with the assurance that the probability of non-coverage is some acceptable value (e.g. 0.05). On the other hand, prediction and tolerance intervals both give information about typical values from the population and the percentage of the population expected to be in the interval. For example, a tolerance interval can be configured to tell us what fraction of sampled values (e.g. 95%) will fall into an interval some fraction of the time (e.g. 95%).

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Predicting with confidence and tolerance. (read)

Altman, N. & Krzywinski, M. (2018) Points of significance: Predicting with confidence and tolerance Nature Methods 15:843–844.

Background reading

Krzywinski, M. & Altman, N. (2013) Points of significance: Importance of being uncertain. Nature Methods 10:809–810.

4-day Circos course

Wed 31-10-2018

A 4-day introductory course on genome data parsing and visualization using Circos. Prepared for the Bioinformatics and Genome Analysis course in Institut Pasteur Tunis, Tunis, Tunisia.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Composite of the kinds of images you will learn to make in this course.

Oryza longistaminata genome cake

Mon 24-09-2018

Data visualization should be informative and, where possible, tasty.

Stefan Reuscher from Bioscience and Biotechnology Center at Nagoya University celebrates a publication with a Circos cake.

The cake shows an overview of a de-novo assembled genome of a wild rice species Oryza longistaminata.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Circos cake celebrating Reuscher et al. 2018 publication of the Oryza longistaminata genome.

Optimal experimental design

Tue 31-07-2018
Customize the experiment for the setting instead of adjusting the setting to fit a classical design.

The presence of constraints in experiments, such as sample size restrictions, awkward blocking or disallowed treatment combinations may make using classical designs very difficult or impossible.

Optimal design is a powerful, general purpose alternative for high quality, statistically grounded designs under nonstandard conditions.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Optimal experimental design. (read)

We discuss two types of optimal designs (D-optimal and I-optimal) and show how it can be applied to a scenario with sample size and blocking constraints.

Smucker, B., Krzywinski, M. & Altman, N. (2018) Points of significance: Optimal experimental design Nature Methods 15:599–600.

Background reading

Krzywinski, M., Altman, N. (2014) Points of significance: Two factor designs. Nature Methods 11:1187–1188.

Krzywinski, M. & Altman, N. (2014) Points of significance: Analysis of variance (ANOVA) and blocking. Nature Methods 11:699–700.

Krzywinski, M. & Altman, N. (2014) Points of significance: Designing comparative experiments. Nature Methods 11:597–598.

The Whole Earth Cataloguer

Mon 30-07-2018
All the living things.

An illustration of the Tree of Life, showing some of the key branches.

The tree is drawn as a DNA double helix, with bases colored to encode ribosomal RNA genes from various organisms on the tree.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
The circle of life. (read, zoom)

All living things on earth descended from a single organism called LUCA (last universal common ancestor) and inherited LUCA’s genetic code for basic biological functions, such as translating DNA and creating proteins. Constant genetic mutations shuffled and altered this inheritance and added new genetic material—a process that created the diversity of life we see today. The “tree of life” organizes all organisms based on the extent of shuffling and alteration between them. The full tree has millions of branches and every living organism has its own place at one of the leaves in the tree. The simplified tree shown here depicts all three kingdoms of life: bacteria, archaebacteria and eukaryota. For some organisms a grey bar shows when they first appeared in the tree in millions of years (Ma). The double helix winding around the tree encodes highly conserved ribosomal RNA genes from various organisms.

Johnson, H.L. (2018) The Whole Earth Cataloguer, Sactown, Jun/Jul, p. 89