Figure Makeover - Live Design Feedback!

Overview

Prior to the event, we accepted submissions from attendees for figures to be redesigned by our talented science designers, so Shiz and Victoria will be demonstrating remaking these figures live for you in BioRender and jam-packing this next session with tons of real-time design tips.

Okay, so this session is called Figure Makeover. Really brave folks have submitted their figures for us to sort of give a makeover to and maybe fix up. You might all have a figure at home in your database that you probably have lying around that you could give a little bit of a fix-up for, and hopefully, we can give you some tips to do that.

So without further ado, let's get started. How we're going to tag team this is Victoria is going to introduce each of the figures that we're going to be making over, and then I'll sort of dive in and kind of give you some design tips on how we would have a nice before and after of that figure.

Before we get started, I wanted to ask a question to the audience, and that is when you're in a different city, what is the number one app that you go to on your phone? If you're in an unfamiliar city or a place, what is your favorite application on your phone on your mobile? It's probably going to be the same for a lot of you folks. And I think the chats are coming in a few seconds delayed here, so I'll give everyone a chance to answer.

Basically, I think it's pretty unanimous, right? Google Maps. So personally, for me, I think Google Maps is like the most powerful, complex product out there. I really admire the product developers on the team there. Think about the amount of information that Google Maps shows. I also actually love that they're using the orange-blue complementary color palette as much as possible. So if you go to this, it is the map of Toronto. They actually stick to a very limited color palette, so all the shops are orange, and stores are blue. The only thing that's red in a Google map search results are the hospitals. So they've really reduced the amount of color that they've selected to show on a map. And as I zoom out, the amount of information that they eliminate, that's really key here. Think of the amount of content that they could have shown, but as I zoom out, you'll notice that they're slowly eliminating content, and that's because you don't need to know that you're in Toronto by the time you kind of zoom into this level. You know, the context is really important. Maybe when I get down to this level, it's important that I start seeing the streets and the houses, but only now can I see the houses, right? I didn't really need to see the individual little squares until I got to that zoom level. So really keep that in mind. I think if Google Maps can do this well, I think we have no excuse to really focus our science figures on something really specific.

So let's dive into like sort of the four main tips that we noticed across all the submissions were common mistakes seen. So, you kind of made our job pretty easy. We noticed a few things that stuck out and we'll just focus on those for the next few minutes here.

Common Design Mistakes

One is reading order. I think Vikki said it well in the previous session; you know, choose a couple of compositions and stick to that. Avoid using excessive boxes. I know that sounds kind of weird, but we actually noticed that quite ubiquitous across all the figures we received. You know, extra design elements here and there that weren't needed. Color, so reduce the variety and number of colors in your figure. Really important. And fourth, here sorry, ensure enough contrast. Really, really important. That is, I would say, the number one mistake I still see in figures if you open up a journal. You know, probably the first thing then is no if you're looking at your figure and you're ability in the directionality of the information.

‍Figure 1

Here's an example of the first figure: So, first submission, maybe I'll hand it over to Vicky here to do a little bit of a spiel of the first figure as I trace out the directionality of this information here.

All right, thanks, Shiz. So, our first figure comes from Natalia, and this is a really detailed overview of the mechanism of action of Cholera Toxin, and here it's showing how that toxin affects intestinal epithelial cells. So, the cholera bacterium, which is in green there at the top right, releases the cholera toxin, which is then in purple. And then, once the toxin is taken up by the cell, you can see that it's illustrated entering the endosomal pathway. And then it traffics through the inside of the cell through the Golgi, and then it reaches the ER. And then eventually, once the toxin reaches the cytoplasm, it activates adenylyl cyclase, and that results in an increase in the production of cyclic AMP. And then that cyclic AMP goes on to act on membrane channels, which ultimately causes the loss of chloride ions. And in the end, what happens is this causes massive fluid secretion in the small intestine, and it leads to severe diarrhea, which if you might already know, is one of the hallmark symptoms of a cholera infection. Natalia’s figure communicates a lot of detailed information and does it really well. But, Shiz, I'm wondering what small adjustments do you think could elevate this one to the next level?

Awesome, thanks Vikki. Basically, what I wanted to show is that this kind of alludes back to that sort of Google Maps analogy of, you know, the story being obviously really, really interesting, and I think Natalia did a really good job of laying out all the foundational elements. So, basically, all we had to do was a little bit of cleanup. You know, remove the intensity of the background. So, again, thinking about Google Maps, you know, I don't have to be reminded that I'm in, you know, say, Toronto, as a city. So, for this, I don't need to be reminded that this is an enterocyte every time I look at the figure.

Thinking about contrast here, if I change it to black and white, I'm noticing that I'm losing some information. The proteins overlaid on the endoplasmic reticulum are getting a little bit lost. The directionality of the reading order, I think, can be improved. So, I'm starting here and I'm going down, looping around, and it kind of does this little bit of a loop and then this fork. So, it's not straightforward. What we did with this composition is we gave it a little bit of a cleanup. And this was Samara, one of our incredible science designers on the team, that helped with it. But, as you can see, we knocked back the enterocyte completely. We reduced the intensity of it, so it's now a nice background, a soft background image. You can see that the reading order is a little smoother. It kind of reads cyclical, so much smoother in the flow of information. I would say this follows our cyclical pathway and the reduction of colors. So again, thinking about Google Maps, where are the really important parts of the story? It's this bacterial occurrence in the exterior of the cell, it goes into the cell, and then out the other end. So, really minimal selection of color going from, I guess, if you look at the before and after side by side, you'll notice a pretty stark difference there. But again, it had all the great ingredients, all we had to do was give it a little bit of a softer feel for the background and reduction of selection of color in the foreground. So even the endoplasmic reticulum, that 3D-looking one, is really nice. It's bright red. All it really needed was this simple 2D outline version. So, that's what I would say, again. Don't shout at your viewer or orient them if they don't need to be. Let that sink into the background and let the main story really take the stage, which I think is happening here on the right. So, I hope that makes sense. Let's see our little cheat sheet here off to the right. I think we followed all the rules here.

Also, sometimes you can add some inspirational elements around the gray area of your canvas in BioRender because if I go to preview, you'll notice that nothing outside of the canvas actually gets rendered or exported. So, it's a really nice way to use it as sort of a workspace as you're creating figures in BioRender.

Figure 2

All right, next submission. All right, so our next figure comes from Pradnya, and I really like this figure because it does such a great job of blending background information on the diabetic bone marrow with the experimental protocol and the treatment results. So, on the left, there's a really nice visual and textual description that probably catches your attention right away of the diabetic bone marrow, and it quickly tells the viewers what's different about the diabetic bone marrow compared to the healthy bone marrow. And then, in the box at the top, there's a really nice stepwise protocol showing how stem cells isolated from teeth are expanded in culture and then transplanted into mice to improve diabetic neuropathy. And then, this here is my favorite part, which is following the arrows down because Pradnya loops everything together by showing us how the experimental treatment in the box improves the diabetic bone marrow and neuropathy that we started with. And this figure does a really nice job of providing that background information and communicating experimental results. But, Shiz, what final touches would you suggest for this one?

Yeah, so what I would do is, again, looking at our cheat sheet of tips, the reading order I think we would look at, the excessive use of maybe boxes, reducing the number of colors and, the variety of colors. So let's take a quick look here. I always like to just give it a quick gut check. Color contrast, when you switch from color to grayscale, do we lose anything? I actually noticed that these cells here, maybe they're mesenchymal cells, the green ones, they actually disappear. So again, the story is super interesting, so I want to make sure that the main areas are going to be focused on. So that probably needs to change the color of the green. Also, green and red, not a really great combo for again our colorblind folks. Let's take our trusty little highlighter and see what the directionality is. So just because there are arrows, it doesn't mean that that's actually the order in which I'm going to be reading the figure. It could be just the boldest thing that catches my eye. It actually started around here, so that's kind of where my eye started. But then there's this title, so I'm probably also going to have some attention up here first. There are arrows coming around that tell me which way to look. And then there's sort of this branching system happening going from left to down and then down on the right here. There is some stuff happening here where there's blood flow coming on about this way. So you can see that the directionality of information is again a little bit messy, but the ingredients are here. So we just have to sort of rejig it a little bit. So let's remove that. And then with the magic of television, we'll go to the final version. So we did a couple of versions actually of this because that's the nature of figure design is that you're going to want to probably make version one, two, three. And that's the nice thing about BioRender Slides is that you can actually have a lot of versions within one file. So here's one version where we've actually flipped the story where, you know, the sort of translation or the applications in the body are in the right here in red. We flipped it back to the beginning there as well. We've also removed the background color. Here's the original again. We've removed background colors. I know it can be tempting to use a background color, but I would really try to avoid that as much as possible, just because it's really hard to play with other colors in your foreground. So we took that out immediately. And ultimately, this is the sort of before and after we went with. I think what was distracting with the original was that we had all these sorts of cells clumping into the bone. Obviously not scientifically accurate, but that wasn't the point of the story. It's, I know it's representational, but I think it was a little bit distracting in that, is it a clogged artery? Is there some sort of tumor? Because that would actually be the size of it in real life. Instead we did this sort of call out where it was a little bit more realistic of the size of the cells. I probably would have even removed the bone completely here and just had the cells there on its own with maybe a red background to show a zoom in of the marrow. We reduce the number of colors. So you can see here from left to right, you know, the number of colors we're showing are greatly drastically reduced. I think the focus is now a little bit cleaner as well. Before, I was kind of looking all over the place, and now the reading order is really sort of like left to right up to down. So a little bit more like that, which is nice. So the before and after, and I think let's see contrast has definitely been improved. So if we again go to our trusty little black and white conversion, you'll notice that the arrows in the previous image were kind of blown out by being very similar in color value. So in the after, what we did was we made the arrows black. You could even make the arrows white to make them stand out a little bit more, like so.

Really bright against that blood vessel. So contrast is really key here when you are dealing with sort of like the mid-tone background color. So before and after, there we go. I think it reads a little bit nicer, and thank you again to our brave submitters for this. Pradnya, we'll send you the final version, and you can use that for your next needs.

Figure 3

Awesome, thanks so much for walking us through that one, Shiz. So our next figure here is coming from Chris, and this is such a simple and elegant visual representation of systems biology. So we start with the DNA there on the left at the smallest scale, and then each step of the diagram goes up one level. So we go from DNA to proteins, and then proteins to networks, networks to cells, and so on all the way until we get to the population level. And it only takes a few seconds of looking at this to immediately understand what Chris was trying to communicate. Shiz, are there any tweaks that you might recommend for this one?

Yeah, so this is tricky because I would have said, you know, it's very clean, very difficult to pick apart. This one, I think they did a lot of good things from the start. What I like to look at is the balance of the intent, the elements. So I actually zoom out and squint, you'll notice that it's pretty heavy along the bottom. This group of people, you know, they're visually darker. It's a larger object, whereas this network up here is a little bit more elegant and thin. I think right away I noticed that these arrows are a little bit sharp, so I probably would have rounded that out a little bit more. And then I think just the variety and intensity of the colors. You know, the heart's quite bright and stark, whereas the body here is a little bit lighter in grayscale.

So what we did was we actually took all of those elements and made it a little bit more cyclical, so that's kind of nice, you know, kind of going with a little bit more of a round composition, and then we actually introduced circles and boxes. So it's going a little bit against our original tip there, so we did that because some figures, if they're so disparate in the way that they look, sometimes give it a unified look and feel. So in this case, you know, the DNA, protein, Network, cell, they all got sort of a nice outline, and this is kind of giving it that uniform look.

We also used a circular arrow here. I love the circular arrows in BioRender because you can actually create a perfect 360-degree arrow, and then you can actually snip it, you can chop it up at certain points. I don't know if you've used that before. Let me do it off to the side here and make it a little bit thicker so you can see. But you know if you want to do something cyclical, you can actually pull down the arrows and snip it at certain points, and you'll actually get a perfect 360-degree I guess almost pathway, and you can chop it up to as many little pieces as you like. If you want to extend it because you actually cut it too short, it'll still follow that exact pattern. You just drag the end there, you notice that I can overlap it. Really neat tool in BioRender. So that's what we implemented here to give it a smoother look. So try out that feature as well. Really cool. Side by side, I think it does read a little bit cleaner. Again, it's not necessary that this entire Krebs cycle was illustrated for one step, so we just removed that, abstracted it, gave it a little bit of a simplified shape.

You know the person. I guess you didn't really have to see the entire body there, but that's a choice you could have made. Shrunk down the population so now everything kind of has equal attention because that's kind of what you want to implement here is equal distribution of attention throughout the whole pathway. So the before and after.

Figure 4

So we've got one more submission here, our final one for the day. Yeah, this one comes from Laura so this is another one about bacteria but this time we're focusing on the penicillin binding protein and that's in purple. Penicillin binding proteins are proteins that are produced by bacteria and they're involved in bacterial cell wall synthesis and they're often membrane-associated which is really nicely shown in that first call out box. And Laura used a really nice Purple Gradient and honestly, I might be a little biased because purple is certainly my favorite color to illustrate different penicillin binding protein homologs. And then at the bottom, we zoom in on those homologs and we look at their susceptibility to different antibiotics. And Laura's done such a nice job at taking us all the way from the bacterium level right down into the protein level. What changes do you think we could make here to make it even better?

Awesome, thanks for that background, Vikki. So what we've done is, again, going back to our little cheat sheet, reducing the number of colors, eliminating some of the boxes. If we think about that again, the Google Maps analogy, the gram-positive cell wall is really prominent. It's a constant reminder again to me that I'm in the bacteria, but if I'm an expert and I'm thinking about penicillin binding proteins, I have that background information so it could barely be noticeable if needed at all. So what we did was, we really reduced the prominence of the bacteria as a background, we reduce the intensity of the bacterial color, and then we removed a couple of other little sort of design elements like the boxes, the call-outs, the intensity of this glow, and then some of the placement of the elements there.

Now I think the flow of information was actually quite good here in Lara's original. So what I did here was, basically, just cleaned up some of the sizing again, the bacteria didn't have to be that big so we kind of made a little bit of a supporting character off to the left. We talk about that, but you know, reducing the transparency sometimes. I know people are afraid to go lighter for background elements, but you'll be surprised how light you can actually get away with background elements. So play with the transparency there and the color. We also reduce the saturation of the green so that the saturation of the foreground important elements which are the proteins are the strongest. Saturation just basically means the purity of the color.

You know, you can actually reduce the saturation with our fancy new color slider here or increase it. You can go from like the highlighter brightness to more of that pastel color and by reducing the saturation, you can actually reduce the attention that it grabs. So that's what we did here. We actually just gave it a flat overlay, it didn't even really matter. I think that they were these sort of sugar rings that are, I think, flipped. That's why it's sort of dark green like green, dark green, light green. For this story specifically, I thought, and again I could be wrong, but I didn't think it was the core of the story, so what we did was, sort of flattened it, just threw it into the background, and so the focus is really the proteins. We also removed these excessive boxes because they were not super necessary to the story. I know we all like to put things in like little clean boxes, but sometimes you just let it breathe and give it a little bit more space, and that actually opens up the negative space in your figure and enables it to look really nice and clean.

So here's the before and after. Let me close up the icon library, and I'm sure if you go into your files now and look at your own figures, you'll notice that you might have too many boxes or too many elements that are producing that. You really clean up the composition.

One little trick we used was a gradient box because when things are zoomed in like that, it actually looks nicer when there's a gradient from one side to another. See if you can notice that gradient there. You can actually make it stronger if you like. You can pull that in, but that way it kind of gives again a little bit more breathing room when you have these call-outs with a fade.

Let's see here. Yeah, I think that's the majority of what we wanted to show. We really give emphasis to the titles so make sure that the hierarchy of text is strong. I do not talk about that in the grant session, but make sure that the main story of the main text is bold, large, and not competing with anything else. In the previous example, here, in the before, the cell wall and cell membrane had almost a title or subtitle level prominence to the font and the darkness. So what we did was we knocked that way back by giving it sort of a green color and reducing the size, reducing the intensity of the color, and immediately the attention gets sent to penicillin binding protein as the title. So I hope that it makes sense where there's a hierarchy of text and you're not competing for attention when the text is the same size or boldness.

Okay, so that's the before and after. So I guess I'm going to wrap up there and thank the brave submitters for entering their figures for this makeover. I will send you all of the before and after images that you can use for your presentations and such. Here's a quick synopsis of the tips themselves: reading order, avoid excessive boxes, reduce the number and the variety of colors you're using, ensure you have enough contrast, again take advantage of the black and white color shifter to really wash it out and see if you've got enough contrast there. And then think about Google Maps. Do you really need to know what your audience needs context for and what they don't need context for? That will clean up your figure quite a bit as you can see. There was commonality amongst all the figures there in those four points.