Here we are now at the middle of the fourth large part of this talk.get nowheremore quotes

# microscopy: tiny

Scientific graphical abstracts — design guidelines

# Creating the Molecular Case Studies Cover

If your photos aren’t good enough, then you’re not close enough
— Robert Capa

Cover design for Apr 2018 issue of Molecular Case Studies. (zoom)

## about the cover

Papillary thyroid carcinoma (PTC) cells, even though malignant, are still genetically programmed to try to be thyroid follicles and may retain their follicular growth pattern, which appear as circles on cross section. Two diagnostic features of papillary thyroid carcinoma are nuclear clearing and intranuclear cytoplasmic inclusions. The black-and-white image is an artistic treatment of a PTC microscopy image (40×) from one of the Personalized Oncogenomics Program study participants at the BC Cancer Research Center. Superimposed is a Circos plot of 17 genomic fusions involving 17 chromosomes identified in the sample by whole-genome sequencing. Showing through the Circos plot is an enhanced color version of the microscopy image. The original image is from Application of genomics to identify therapeutic targets in recurrent pediatric papillary thyroid carcinoma by Ronsley et al. in the April 2018 issue.

The theme of the April issue of Molecular Case Studies is precision oncogenomics. We have three papers in the issue based on work done in our Personalized Oncogenomics Program (POG).

...this special issue provide[s] a glimpse into current cancer precision medicine efforts, reflecting only a microcosm of ... genomics in this bustling space of clinical translation.
John C. Carpten & Elaine R. Mardis
The era of precision oncogenomics
Mol. Case Stud. (2018) 4(2).

I've previously created art based on POG data—posters to celebrate the program's 5-year anniversary.

## input materials

The covers of Molecular Case Studies typically show microscopy images, with some shown in a more abstract fashion. There's also the occasional Circos plot.

I've previously taken a more fine-art approach to cover design, such for those of Nature, Genome Research and Trends in Genetics. I've used microscopy images to create a cover for PNAS—the one that made biology look like astrophysics—and thought that this is kind of material I'd start with for the MCS cover.

A few of the microscopy slides submitted to me for the cover design. Courtesy of Anna Lee (Dept Pathology and Laboratory Medicine, UBC).

When I look at these kind of images, I have basically no idea what I'm looking at. Sure, I know this is life at tiny scale but I am not a pathologist. This helps me greatly.

Instead, I see color, shapes, and contrast. I hunt for patterns that would make for an interesting visual, without necessarily trying to communicate any of the science behind that—the paper does a much better job at this than I ever could. It's largely a process driven by intuition and my desire to see distinct visual patterns at different length scales with some symmetry, ideally broken in a pleasing way. Vague, I know.

Images of different regions of the same slide, at the same magnification, can have very different levels of visual engagement (for the non-specialist). Just compare the two images below.

Same magnification, same slide. The image on the right is interesting. The one on the left is not, artistically speaking. Courtesy of Anna Lee (Dept Pathology and Laboratory Medicine, UBC).

The slide on the left really caught my eye. It had the right proportion of tiny, small, medium and large things.

I see a heart, a face and lava flow among faces. Obviously, faces everywhere—humans are good at those kinds of Type I errors. The panels below are 100% crops of the 40× slide of papillary thyroid carcinoma shown above them. Courtesy of Anna Lee (Dept Pathology and Laboratory Medicine, UBC).

## black and white version

The black-and-white version was obtained by solarizing the image. There are both color and black-and-white options for solarization, a method in which various tones of the image are remapped in brightness.

(A) The original slide (B) A black-and-white composition using Nik Color Efex 4 filters applied in succession to the slide: dark contrast, tonal contrast, white neutralizer and solarization.
Compounding effects of each of the filters on the image above.

And here's the first black-and-white take.

The initial black-and-white composition after applying Nik filters.

This looked good but a bit dark. I handled this by lightening the tone, differently depending on the element in the image. I also wanted to bring out more details in the internal structure of the cells. This was achieved by applying an otherwise aggressive sharpening mask.

The effect of additional sharpening and tone remaps, applied differently to intracellular and extracellular regions.

I was quite happy with this result. The combination of solarization and sharpening created a large variety of patterns inside the cells. My brain fought hard to see faces in them.

100% crops of regions of the above black-and-white image. I see a heart (this is the same heart region shown in the color crop above), then a some kind of dog/cat chimera, in the last panel, a suprrised or scared camel. If you look very carefully, you can see a grumpy cat coming out of the heart.

Because I had slides at different magnifications, I created a design in which three slides at 10, 20 and 40 × were composited together so that from left to right the magnification increased across the image. The effect is subtle—you can easily miss it, which is the point.

A seamless stitch of black-and-white treatments of 10, 20 and 40 × slides. As you go from left to right, the magnification increases.

I had pretty high hopes for these black-and-white versions. Previous covers in MCS have been colorful, though, so I thought to provide a color option.

## color version

For the color version, I wanted to give the colors more punch. For sure.

I also wanted to emphasize the details, like for the black-and-white image.

The first process step of the color slide was done using 5 Nik filters, applied in succession: dark contrast, tonal contrast, sunlight, polarization and detail extractor. The effects of the stack of these filters is shown on the original image below. The whole image is shown and in each strip the filters are stacked.

The effect of stacking 5 Nik filters on the original image.

Here's the full image with the 5 Nik filters applied.

A seamless stitch of black-and-white treatments of 10, 20 and 40 × slides. As you go from left to right, the magnification increases.

Not there yet, though. I added more sharpening (more than I've ever used before, so I felt a little weird, but got over it quickly). The colors were punched up too—I wanted more contrast between the blue and red areas and transform the reds a little into oranges.

A seamless stitch of black-and-white treatments of 10, 20 and 40 × slides. As you go from left to right, the magnification increases.

If it looks like the blue areas are popping out of the image, that's the effect of the emboss filter.

## final composition

The editors asked me to encorporate a Circos image in the final design. This was tricky—I had spent a lot of time up to now fiddling with extracting patterns and textures from the images.

Something as geometrical and rational as a data graphic would alter the personality of the design. But, the goal of artistic collaboration is always to find a way, so I took some gene fusions that were found in the sample with our structural variant pipeline and created a bare-bones Circos image out of them.

A seamless stitch of black-and-white treatments of 10, 20 and 40 × slides. As you go from left to right, the magnification increases.

This was then superimposed on the image and emphasized by using the color design inside the circle and black-and-white design outside.

The final composition for the cover combines both black-and-white and color treatments. The colored pattern stands out above the black-and-white background.

It's always fun to invert images and see what happens.

Inverse of the above. Notice how the pattern inside the circle appears to be sitting below the plane, making the circle more of a window to a scene. .

# Graphical Abstract Design Guidelines

Fri 13-11-2020

Clear, concise, legible and compelling.

Making a scientific graphical abstract? Refer to my practical design guidelines and redesign examples to improve organization, design and clarity of your graphical abstracts.

Graphical Abstract Design Guidelines — Clear, concise, legible and compelling.

# "This data might give you a migrane"

Tue 06-10-2020

An in-depth look at my process of reacting to a bad figure — how I design a poster and tell data stories.

A poster of high BMI and obesity prevalence for 185 countries.

# He said, he said — a word analysis of the 2020 Presidential Debates

Thu 01-10-2020

Building on the method I used to analyze the 2008, 2012 and 2016 U.S. Presidential and Vice Presidential debates, I explore word usagein the 2020 Debates between Donald Trump and Joe Biden.

Analysis of word usage by parts of speech for Trump and Biden reveals insight into each candidate.

# 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!

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.

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.

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.

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.

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.