music + dance + projected visualsmarvel at perfect timingmore quotes

# space: exciting

DNA on 10th — street art, wayfinding and font

# 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)
VIEW ALL

# Scientific data visualization: Aesthetic for diagrammatic clarity

Mon 13-01-2020

The scientific process works because all its output is empirically constrained.

My chapter from The Aesthetics of Scientific Data Representation, More than Pretty Pictures, in which I discuss the principles of data visualization and connect them to the concept of "quality" introduced by Robert Pirsig in Zen and the Art of Motorcycle Maintenance.

# Yearning for the Infinite — Aleph 2

Mon 18-11-2019

Discover Cantor's transfinite numbers through my music video for the Aleph 2 track of Max Cooper's Yearning for the Infinite (album page, event page).

Yearning for the Infinite, Max Cooper at the Barbican Hall, London. Track Aleph 2. Video by Martin Krzywinski. Photo by Michal Augustini. (more)

I discuss the math behind the video and the system I built to create the video.

# Hidden Markov Models

Mon 18-11-2019

Everything we see hides another thing, we always want to see what is hidden by what we see.
—Rene Magritte

A Hidden Markov Model extends a Markov chain to have hidden states. Hidden states are used to model aspects of the system that cannot be directly observed and themselves form a Markov chain and each state may emit one or more observed values.

Hidden states in HMMs do not have to have meaning—they can be used to account for measurement errors, compress multi-modal observational data, or to detect unobservable events.

Nature Methods Points of Significance column: Hidden Markov Models. (read)

In this column, we extend the cell growth model from our Markov Chain column to include two hidden states: normal and sedentary.

We show how to calculate forward probabilities that can predict the most likely path through the HMM given an observed sequence.

Grewal, J., Krzywinski, M. & Altman, N. (2019) Points of significance: Hidden Markov Models. Nature Methods 16:795–796.

Hola Mundo by Hannah Fry. Cover design is based on my 2013 $\pi$ day art. (read)