Tango is a sad thought that is danced.think & dance

# space: exciting

Workshop at Brain and Mind Symposium, Långvik Congress Center, Kirkkonummi, Sep 17–18 2015.

# visualization + design

Cover image accompanying our article on mouse vasculature development. Biology turns astrophysical. PNAS 1 May 2012; 109 (18) (zoom, PNAS)

# Creating the PNAS Cover

One of my goals in life, which I can now say has been accomplished, is to make biology look like astrophysics. Call it my love for the Torino Impact Hazard Scale.

Recently, I was given an opportunity to attend to this (admittedly vague) goal when Linda Chang from Aly Karsan's group approached me with some microscopy photos of mouse veins. I was asked to do "something" with these images for a cover submission to accompany the manuscript.

When people see my covers, sometimes they ask "How did you do that?" Ok, actually they never ask this. But being a scientist, I'm trained me to produce answers in anticipation of such questions. So, below, I show you how the image was constructed.

The image was published on the cover of PNAS (PNAS 1 May 2012; 109 (18))

## Tools

Photoshop CS5, Nik Color Efex Pro 4, Alien Skin Bokeh 2 and a cup of coffee from a Rancilio Silvia.

## source images

Below are a few of the images I had the option to work with. These are mouse embryonic blood vessels, with a carotid artery shown in the foreground with endothelial cells in green, vascular smooth muscle cells in red and the nuclei in blue.

Of course, as soon as I saw the images, I realized that there was very little that I needed to do to trigger the viewer's imagination. These photos were great!

Mouse carotid arteries. (zoom)
Mouse carotid arteries. (zoom)
Mouse carotid arteries. (zoom)
Mouse carotid arteries. (zoom)
Mouse carotid arteries. (zoom)
Mouse carotid arteries. (zoom)
Mouse carotid arteries. (zoom)
Mouse carotid arteries. (zoom)
Mouse carotid arteries. (zoom)

## memories of star trek

Immediately I thought of two episodes of Star Trek (original series): Doomsday Machine and the Immunity Syndrome, as well as of images from the Hubble Telescope.

Enterprise is about to be consumed by a horror tube: a planet killer! (The Doomsday Machine)
Enterprise heads into a giant amoeba. Who eats whom? I'll let you guess. (The Immunity Syndrome)
Orion nebula (M42) as seen by the Hubble telescope. (zoom)

I though it would be pretty easy to make the artery images look all-outer-spacey. They already looked it.

## centerpiece image

And then I saw the image below.

A particularly spectacular image of a mouse carotid artery. I'm thinking 10 on the Torino scale. (zoom)

## constructing the cover

### background

The background was created from the two images shown here. The second image was sampled three times, at different rotations.

Images used for background. (zoom)
Images used for background. (zoom)
Layer composition for background elements. (zoom)

The channel mixer was used to remove the green channel and leave only red and blue.

Background elements for PNAS cover image. (zoom)

### middle ground

The next layer was composed of what looked like ribbons of blue gas. This was created by sampling the oval shapes from the source images. Here the red channel was a great source for cloud shapes, and this was the only channel that was kept. The hue was shifted to blue and a curve adjustment was applied to increase the contrast.

First set of middle ground elements, before adjustments. (zoom)
First set of middle ground elements, after channel adjustments. (zoom)
Second set of middle ground elements. (zoom)
Layer composition for middle ground elements. (zoom)

When the foreground and middle ground elements were combined, the result was already 40 parsecs away.

Background and foreground elements for PNAS cover image. (zoom)

### foreground

The foreground was created from the spectacular comet-like image of a mouse artery. Very little had to be done to make this element look good. It already looked good.

I applied a little blur using Alien Skin's Bokeh 2 to narrow the apparent depth of field, masked out elements at the bottom of the image and removed some of the green channel. The entire blue channel was removed altogether (this gave the tail of the comet a mottled, flame-like appearance).

Foreground element, after channel adjustments. (zoom)
Layer composition for foreground element. (zoom)

### post processing

Initial composition of background, middle ground and foreground elements. (zoom)
40% localized application of Nik's Tonal Contrast (Color Efex 4 plugin) to increase structure in red channel. (zoom)
50% blend with Nik's Pro Contrast (Color Efex 4 plugin). (zoom)

And here we have the final image.

Final PNAS cover. Spacey! (zoom)

# Bayes' Theorem

Wed 22-04-2015

In our first column on Bayesian statistics, we introduce conditional probabilities and Bayes' theorem

P(B|A) = P(A|B) × P(B) / P(A)

This relationship between conditional probabilities P(B|A) and P(A|B) is central in Bayesian statistics. We illustrate how Bayes' theorem can be used to quickly calculate useful probabilities that are more difficult to conceptualize within a frequentist framework.

Nature Methods Points of Significance column: Bayes' Theorem. (read)

Using Bayes' theorem, we can incorporate our beliefs and prior experience about a system and update it when data are collected.

Puga, J.L, Krzywinski, M. & Altman, N. (2015) Points of Significance: Bayes' Theorem Nature Methods 12:277-278.

Oldford, R.W. & Cherry, W.H. Picturing probability: the poverty of Venn diagrams, the richness of eikosograms. (University of Waterloo, 2006)

# Happy 2015 Pi Day—can you see pi through the treemap?

Sat 14-03-2015

Celebrate pi Day (March 14th) with splitting its digit endlessly. This year I use a treemap approach to encode the digits in the style of Piet Mondrian.

Digits of pi, phi and e. (details)

The art has been featured in Ana Swanson's Wonkblog article at the Washington Post—10 Stunning Images Show The Beauty Hidden in pi.

I also have art from 2013 pi Day and 2014 pi Day.

# Split Plot Design

Tue 03-03-2015

The split plot design originated in agriculture, where applying some factors on a small scale is more difficult than others. For example, it's harder to cost-effectively irrigate a small piece of land than a large one. These differences are also present in biological experiments. For example, temperature and housing conditions are easier to vary for groups of animals than for individuals.

Nature Methods Points of Significance column: Split plot design. (read)

The split plot design is an expansion on the concept of blocking—all split plot designs include at least one randomized complete block design. The split plot design is also useful for cases where one wants to increase the sensitivity in one factor (sub-plot) more than another (whole plot).

Altman, N. & Krzywinski, M. (2015) Points of Significance: Split Plot Design Nature Methods 12:165-166.

1. Krzywinski, M. & Altman, N. (2014) Points of Significance: Designing Comparative Experiments Nature Methods 11:597-598.

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

3. Blainey, P., Krzywinski, M. & Altman, N. (2014) Points of Significance: Replication Nature Methods 11:879-880.

# Color palettes for color blindness

Tue 03-03-2015

In an audience of 8 men and 8 women, chances are 50% that at least one has some degree of color blindness1. When encoding information or designing content, use colors that is color-blind safe.

A 12-color palette safe for color blindness