syncopation & accordionlike France, but no dog poopmore quotes

# making poetry out of spam is fun

EMBO Practical Course: Bioinformatics and Genome Analysis, 5–17 June 2017.

# 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)
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# Happy 2017 $\pi$ Day—Star Charts, Creatures Once Living and a Poem

Tue 14-03-2017

on a brim of echo,

capsized chamber
drawn into our constellation, and cooling.
—Paolo Marcazzan

Celebrate $\pi$ Day (March 14th) with star chart of the digits. The charts draw 40,000 stars generated from the first 12 million digits.

12,000,000 digits of $\pi$ interpreted as a star catalogue. (details)

The 80 constellations are extinct animals and plants. Here you'll find old friends and new stories. Read about how Desmodus is always trying to escape or how Megalodon terrorizes the poor Tecopa! Most constellations have a story.

Find friends and stories among the 80 constellations of extinct animals and plants. Oh look, a Dodo guardings his eggs! (details)

This year I collaborate with Paolo Marcazzan, a Canadian poet, who contributes a poem, Of Black Body, about space and things we might find and lose there.

Check out art from previous years: 2013 $\pi$ Day and 2014 $\pi$ Day, 2015 $\pi$ Day and and 2016 $\pi$ Day.

# Data in New Dimensions: convergence of art, genomics and bioinformatics

Tue 07-03-2017

Art is science in love.
— E.F. Weisslitz

A behind-the-scenes look at the making of our stereoscopic images which were at display at the AGBT 2017 Conference in February. The art is a creative collaboration with Becton Dickinson and The Linus Group.

Its creation began with the concept of differences and my writeup of the creative and design process focuses on storytelling and how concept of differences is incorporated into the art.

Oh, and this might be a good time to pick up some red-blue 3D glasses.

A stereoscopic image and its interpretive panel of single-cell transcriptomes of blood cells: diseased versus healthy control.

# Interpreting P values

Thu 02-03-2017
A P value measures a sample’s compatibility with a hypothesis, not the truth of the hypothesis.

This month we continue our discussion about $P$ values and focus on the fact that $P$ value is a probability statement about the observed sample in the context of a hypothesis, not about the hypothesis being tested.

Nature Methods Points of Significance column: Interpreting P values. (read)

Given that we are always interested in making inferences about hypotheses, we discuss how $P$ values can be used to do this by way of the Benjamin-Berger bound, $\bar{B}$ on the Bayes factor, $B$.

Heuristics such as these are valuable in helping to interpret $P$ values, though we stress that $P$ values vary from sample to sample and hence many sources of evidence need to be examined before drawing scientific conclusions.

Altman, N. & Krzywinski, M. (2017) Points of Significance: Interpreting P values. Nature Methods 14:213–214.

Krzywinski, M. & Altman, N. (2017) Points of significance: P values and the search for significance. Nature Methods 14:3–4.

Krzywinski, M. & Altman, N. (2013) Points of significance: Significance, P values and t–tests. Nature Methods 10:1041–1042.

# Snellen Charts—Typography to Really Look at

Sat 18-02-2017

Another collection of typographical posters. These ones really ask you to look.

Snellen charts designed using physical constants, Braille and elemental abundances in the universe and human body.

The charts show a variety of interesting symbols and operators found in science and math. The design is in the style of a Snellen chart and typset with the Rockwell font.