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

# cells: small

In Silico Flurries: Computing a world of snow. Scientific American. 23 December 2017

# 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)

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. .
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# Two-level factorial experiments

Fri 22-03-2019
To find which experimental factors have an effect, simultaneously examine the difference between the high and low levels of each.

Two-level factorial experiments, in which all combinations of multiple factor levels are used, efficiently estimate factor effects and detect interactions—desirable statistical qualities that can provide deep insight into a system.

They offer two benefits over the widely used one-factor-at-a-time (OFAT) experiments: efficiency and ability to detect interactions.

Nature Methods Points of Significance column: Two-level factorial experiments. (read)

Since the number of factor combinations can quickly increase, one approach is to model only some of the factorial effects using empirically-validated assumptions of effect sparsity and effect hierarchy. Effect sparsity tells us that in factorial experiments most of the factorial terms are likely to be unimportant. Effect hierarchy tells us that low-order terms (e.g. main effects) tend to be larger than higher-order terms (e.g. two-factor or three-factor interactions).

Smucker, B., Krzywinski, M. & Altman, N. (2019) Points of significance: Two-level factorial experiments Nature Methods 16:211–212.

Krzywinski, M. & Altman, N. (2014) Points of significance: Designing comparative experiments.. Nature Methods 11:597–598.

# Happy 2019 $\pi$ Day—Digits, internationally

Tue 12-03-2019

Celebrate $\pi$ Day (March 14th) and set out on an exploration explore accents unknown (to you)!

This year is purely typographical, with something for everyone. Hundreds of digits and hundreds of languages.

A special kids' edition merges math with color and fat fonts.

116 digits in 64 languages. (details)
223 digits in 102 languages. (details)

Check out art from previous years: 2013 $\pi$ Day and 2014 $\pi$ Day, 2015 $\pi$ Day, 2016 $\pi$ Day, 2017 $\pi$ Day and 2018 $\pi$ Day.

# Tree of Emotional Life

Sun 17-02-2019

One moment you're $:)$ and the next you're $:-.$

Make sense of it all with my Tree of Emotional life—a hierarchical account of how we feel.

A section of the Tree of Emotional Life.

# Find and snap to colors in an image

Sat 29-12-2018

One of my color tools, the $colorsnap$ application snaps colors in an image to a set of reference colors and reports their proportion.

Below is Times Square rendered using the colors of the MTA subway lines.

Colors used by the New York MTA subway lines.

Times Square in New York City.
Times Square in New York City rendered using colors of the MTA subway lines.
Granger rainbow snapped to subway lines colors from four cities. (zoom)

# Take your medicine ... now

Wed 19-12-2018

Drugs could be more effective if taken when the genetic proteins they target are most active.

Design tip: rediscover CMYK primaries.

More of my American Scientific Graphic Science designs

Ruben et al. A database of tissue-specific rhythmically expressed human genes has potential applications in circadian medicine Science Translational Medicine 10 Issue 458, eaat8806.

# Predicting with confidence and tolerance

Wed 07-11-2018
I abhor averages. I like the individual case. —J.D. Brandeis.

We focus on the important distinction between confidence intervals, typically used to express uncertainty of a sampling statistic such as the mean and, prediction and tolerance intervals, used to make statements about the next value to be drawn from the population.

Confidence intervals provide coverage of a single point—the population mean—with the assurance that the probability of non-coverage is some acceptable value (e.g. 0.05). On the other hand, prediction and tolerance intervals both give information about typical values from the population and the percentage of the population expected to be in the interval. For example, a tolerance interval can be configured to tell us what fraction of sampled values (e.g. 95%) will fall into an interval some fraction of the time (e.g. 95%).

Nature Methods Points of Significance column: Predicting with confidence and tolerance. (read)

Altman, N. & Krzywinski, M. (2018) Points of significance: Predicting with confidence and tolerance Nature Methods 15:843–844.