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# mouse veins: exciting

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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# $k$ index: a weightlighting and Crossfit performance measure

Wed 07-06-2017

Similar to the $h$ index in publishing, the $k$ index is a measure of fitness performance.

To achieve a $k$ index for a movement you must perform $k$ unbroken reps at $k$% 1RM.

The expected value for the $k$ index is probably somewhere in the range of $k = 26$ to $k=35$, with higher values progressively more difficult to achieve.

In my $k$ index introduction article I provide detailed explanation, rep scheme table and WOD example.

# Dark Matter of the English Language—the unwords

Wed 07-06-2017

I've applied the char-rnn recurrent neural network to generate new words, names of drugs and countries.

The effect is intriguing and facetious—yes, those are real words.

But these are not: necronology, abobionalism, gabdologist, and nonerify.

These places only exist in the mind: Conchar and Pobacia, Hzuuland, New Kain, Rabibus and Megee Islands, Sentip and Sitina, Sinistan and Urzenia.

And these are the imaginary afflictions of the imagination: ictophobia, myconomascophobia, and talmatomania.

And these, of the body: ophalosis, icabulosis, mediatopathy and bellotalgia.

Want to name your baby? Or someone else's baby? Try Ginavietta Xilly Anganelel or Ferandulde Hommanloco Kictortick.

When taking new therapeutics, never mix salivac and labromine. And don't forget that abadarone is best taken on an empty stomach.

And nothing increases the chance of getting that grant funded than proposing the study of a new –ome! We really need someone to looking into the femome and manome.

# Dark Matter of the Genome—the nullomers

Wed 31-05-2017

An exploration of things that are missing in the human genome. The nullomers.

Julia Herold, Stefan Kurtz and Robert Giegerich. Efficient computation of absent words in genomic sequences. BMC Bioinformatics (2008) 9:167

# Clustering

Wed 31-05-2017
Clustering finds patterns in data—whether they are there or not.

We've already seen how data can be grouped into classes in our series on classifiers. In this column, we look at how data can be grouped by similarity in an unsupervised way.

Nature Methods Points of Significance column: Clustering. (read)

We look at two common clustering approaches: $k$-means and hierarchical clustering. All clustering methods share the same approach: they first calculate similarity and then use it to group objects into clusters. The details of the methods, and outputs, vary widely.

Altman, N. & Krzywinski, M. (2017) Points of Significance: Clustering. Nature Methods 14:545–546.