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Trance opera—Spente le Stellebe dramaticmore quotes


The Outbreak Poems — artistic emissions in a pandemic


visualization + design

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
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!

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Mouse carotid arteries. (zoom)
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Mouse carotid arteries. (zoom)
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Mouse carotid arteries. (zoom)
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Mouse carotid arteries. (zoom)
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Mouse carotid arteries. (zoom)
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Mouse carotid arteries. (zoom)
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Mouse carotid arteries. (zoom)
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Mouse carotid arteries. (zoom)
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
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.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Enterprise is about to be consumed by a horror tube: a planet killer! (The Doomsday Machine)
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Enterprise heads into a giant amoeba. Who eats whom? I'll let you guess. (The Immunity Syndrome)
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
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.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
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.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Images used for background. (zoom)
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Images used for background. (zoom)
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Layer composition for background elements. (zoom)

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

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
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.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
First set of middle ground elements, before adjustments. (zoom)
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
First set of middle ground elements, after channel adjustments. (zoom)
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Second set of middle ground elements. (zoom)
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Layer composition for middle ground elements. (zoom)

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

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
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).

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Foreground element, before adjustments. (zoom)
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Foreground element, after channel adjustments. (zoom)
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Layer composition for foreground element. (zoom)

post processing

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

And here we have the final image.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Final PNAS cover. Spacey! (zoom)

VIEW ALL

news + thoughts

Points of Significance celebrates 50th column

Mon 24-08-2020

We are celebrating the publication of our 50th column!

To all our coauthors — thank you and see you in the next column!

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance: Celebrating 50 columns of clear explanations of statistics. (read)

Uncertainty and the management of epidemics

Mon 24-08-2020

When modelling epidemics, some uncertainties matter more than others.

Public health policy is always hampered by uncertainty. During a novel outbreak, nearly everything will be uncertain: the mode of transmission, the duration and population variability of latency, infection and protective immunity and, critically, whether the outbreak will fade out or turn into a major epidemic.

The uncertainty may be structural (which model?), parametric (what is `R_0`?), and/or operational (how well do masks work?).

This month, we continue our exploration of epidemiological models and look at how uncertainty affects forecasts of disease dynamics and optimization of intervention strategies.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Uncertainty and the management of epidemics. (read)

We show how the impact of the uncertainty on any choice in strategy can be expressed using the Expected Value of Perfect Information (EVPI), which is the potential improvement in outcomes that could be obtained if the uncertainty is resolved before making a decision on the intervention strategy. In other words, by how much could we potentially increase effectiveness of our choice (e.g. lowering total disease burden) if we knew which model best reflects reality?

This column has an interactive supplemental component (download code) that allows you to explore the impact of uncertainty in `R_0` and immunity duration on timing and size of epidemic waves and the total burden of the outbreak and calculate EVPI for various outbreak models and scenarios.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Uncertainty and the management of epidemics. (Interactive supplemental materials)

Bjørnstad, O.N., Shea, K., Krzywinski, M. & Altman, N. (2020) Points of significance: Uncertainty and the management of epidemics. Nature Methods 17.

Background reading

Bjørnstad, O.N., Shea, K., Krzywinski, M. & Altman, N. (2020) Points of significance: Modeling infectious epidemics. Nature Methods 17:455–456.

Bjørnstad, O.N., Shea, K., Krzywinski, M. & Altman, N. (2020) Points of significance: The SEIRS model for infectious disease dynamics. Nature Methods 17:557–558.

Cover of Nature Genetics August 2020

Mon 03-08-2020

Our design on the cover of Nature Genetics's August 2020 issue is “Dichotomy of Chromatin in Color” . Thanks to Dr. Andy Mungall for suggesting this terrific title.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Dichotomy of Chromatin in Color. Nature Genetics, August 2020 issue. (read more)

The cover design accompanies our report in the issue Gagliardi, A., Porter, V.L., Zong, Z. et al. (2020) Analysis of Ugandan cervical carcinomas identifies human papillomavirus clade–specific epigenome and transcriptome landscapes. Nature Genetics 52:800–810.

Poster Design Guidelines

Wed 15-07-2020

Clear, concise, legible and compelling.

The PDF template is a poster about making posters. It provides design, typography and data visualiation tips with minimum fuss. Follow its advice until you have developed enough design sobriety and experience to know when to go your own way.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Poster Design Guidelines — Clear, concise, legible and compelling..