BioRender 201 - New & Advanced Features!

Overview

Hello everyone. As Jeff mentioned, my name is Francesca, and I'm just gonna walk you through some of our newer and more advanced features, building on some of the concepts that Jacqueline already touched on.

So basically what we'll cover today, I sectioned it off to four major features that I thought were super relevant with either customization or saving time. So the first two are multi-select and alignment tools that I'm going to go through with you. The second two are kind of customization tools for shapes and lines. I'm also going to be covering two new features of connector lines and custom icon colors, which I'm super excited to show you today as well.

Alright, so let's dive into some of these advanced features. I'm gonna go and start with saving time with some of our multi-select and alignment tools.

Multi-select 

So if you're ever in a situation where you have a lot of something in an environment, whether that's cytokines or antibodies, maybe even cells in a solution, this feature really saves you time. Say you wanted to edit all of these antibodies at once, instead of selecting each of them one by one like this and then maybe changing the color, if you did want to say change all of these antibodies to like a red or a purple color, we have this really cool feature, and I'll show you how to do it. You just right-click on it, and then select all the same icons, and this actually selects every single type of that icon across your whole canvas so that you can edit it and change it all together. So if I wanted to make it red or purple, I can go ahead and do that instead of trying to change one by one over here. And I'll show you how to do a more detailed version of this in a bit, but for example in this scenario, you could have probably highlighted all of these and changed it all together, but there are certain scenarios where this is really, really helpful.

So one of those examples is the tumor microenvironment where maybe you have a lot of these like immune cells and cancer cells all bunched up together and kind of the nightmare of trying to change every single one of these cancer cells one by one. We've kind of eliminated that for you, so that you can right-click on it again, select all of the same icons, and it'll even select the one in my Legend too, so it's across your whole canvas, and then you can change it all together like this.

While you're picking the color here for any of these images, I'm going to be throwing in a little bit of design tips and tricks as well. So for example, for this image, our cancer cells are in this green color, and our immune cells are more in this reddish color. And if you recall, a lot of times like reading story books or comic books as a kid, a lot of times if you have a really obvious bad guy versus good guys, like an antagonist versus protagonist in your story, you can usually see that a lot of these bad guys are this like reddish tone. And even in this image here, of this like Darth Vader fighting with Luke Skywalker, you can see even in their lightsabers, it's like red versus green. And these concepts are used a lot in storytelling, and you can also use these in your scientific images as well. So good guys like more of this coolish, greenish, bluish tone.

Here are some more examples from our favorite characters back in the day. Disney and Pixar do this a lot using color concepts to kind of low-key tell their stories as well. And you can see that red usually denotes dangerous stuff and bad. So I'm keeping this in mind going back to our figure as well over here with this tumor microenvironment. We can now see that there's this cancer cell which is obviously a very bad guy. So I'm gonna go ahead and change this not from a green color but more to maybe like a reddish tone. So we have a few options over here, maybe I'll use this one for now. And these immune cells just based on the color look kind of scary. So immune and dendritic cells are actually really good cells for your body. So I'm gonna go ahead and change that maybe to more of a greenish color. And then these are macro features, so maybe I'll change that to a blue color.

And just like that, even looking at this image from not even changing any words or composition, just from color, you can see that a lot of the storytelling has become a bit more clear in this tumor microenvironment image. Yeah, so that's just one way you can use this feature and then also keep those color concepts in mind.

Next thing I wanted to touch on is things like this. So I like the way this protocol is laid out and it looks really nice. It's really nicely organized, but I do have this protein of interest over here that I want to really focus on, and I want my readers to focus on over here as well. But it's kind of fading in or blending in with all the other elements just because it's that blue color and a lot of the other icons in this image are also blue. So what I'm going to do is I'm actually going to select all of the same icons again like we did previously.

It's going to select all of them and all of these different zoom-in boxes, even this purification one. And why don't we go ahead and change this color to more of an orange color? And I'm choosing orange actually because orange is a complementary color to blue. So if you recall like color wheels and learning about that as a kid when I say complementary color, it just means any color that's on the opposite end of the color wheel. So kind of red to green over here, blue to orange or purple to yellow. And when these colors are placed next to each other, they actually create a really strong contrast and it lets the other one pop out a lot more. And that's why I'm choosing orange against the blue background here.

I've seen a lot of companies actually do this for their logos because you want logos to stand out a lot. So you see like the blue on orange here, the red on green, maybe the yellow with the purple. So these are kind of real-life examples where you can also use to make your images, whether that's a protein of interest, whether that's like part of your DNA, really pop and stand out. I hope that's clear. Let me know if you have any questions. I do have the chat open on the right-hand side of my screen. So if you have any other questions, let me know, and I'm happy to go through that as well.

Alignment 

All right, so besides color-saving and saving time with colors, this feature can also help with alignment tools. So, if you have a situation like this where all my cells are kind of scattered around my canvas, instead of aligning it one by one like this, what I can also do is just right-click on it, again select all the same icons, and we actually have this cool alignment feature at the top toolbar over here. You can distribute it evenly so that all the cells are evenly spaced out, and then you can also align them all to the center, really easy in a few seconds, two different steps. You can make them all align really perfectly, so I just find that that's a feature that has saved me so much time in the past, and this is pretty simple, it's just like five blood cells over here, but if you look at examples like this, where you're working with protocols and it becomes a longer stretch of icons, even like these boxes, instead of trying to align, you know, pixel push all of these one pixel at a time, all you have to do is just select all of them, again distribute it over here, just repeating what we covered, and then align them all together, so you don't have to actually do it one by one. So, that was just like select all and distribute, has saved me so much time, I wanted to share that with you as well for one of our advanced features, and I hope that's clear, let me know if you have any questions about that and I can move on to the next over here.

The next tip I have is for customization, so we have a lot of different customization tools like shapes and lines in BioRender. I know there are some questions about it in the chat as well, which I can cover now, but the first thing I wanted to cover was a tool, I guess internally we call it the custom blob tool. I don't know if there's an official name for it because you can correct me if I'm wrong, but I call it the custom blob tool. It's kind of a funny name, but it's all of these customized tools over here, and they all kind of behave very similarly, so I'm just going to touch on one of them. I won't go through every single one, but these are super, super cool tools if you don't have as much of a steady hand with your mouse as I do. I've seen our illustrators draw everything freehand, but I don't know if I can do that, so I use this tool a lot to just kind of drag around and make any custom shapes that I need to.

Over here, you can see a lot of different notes. Some of them are filled in blue, those are your existing anchor points, and some of them are white, and you can drag these out to make a new anchor point, and every time you drag one out, a new one appears, and you can infinitely start editing and creating any shape that you need to over here, whether that's like a weird jelly bean shape or squiggles, anything you need over here. And then you can even further edit and customize all the borders and the fills, kind of similar to the ‘Bio-brushes’ that Jacqueline covered, but more in a shape version. You're probably wondering where you might use this tool. It's kind of a weird tool. It looks pretty funny, and one area where you can actually use it is places like this. So, I've seen it, and it doesn't only have to be for the brain, it can be for babies, livers, or any other icon types really when you want to highlight specific areas of that. You can go ahead and use that. So, why don't I go ahead and show you that?

Custom Shapes

I personally like the brain because it's a very lobular structure. I feel like it's really good for this, and if there are any neuroscientists in the room, I think you'll appreciate this as well. But, yeah, if you want to highlight any sites of any of your icons, maybe you're making a lesion in the brain, or maybe there's like a tumor that's affecting a large area, even like active sites, maybe you administered a drug and you know the frontal lobe of the brain is a lot more active than the back, and you want to show that, that's something that you can do with this tool as well, really easily over here. So, maybe this is solely the area I want. I can even go really in detail and zoom in and make it really sensitive in terms of making more nodes and highlighting individual lobes over here. I won't do that for the purposes of our demo, just to save some time, but just feel free to go around, play around with it.

One thing I would do from here as well, instead of just throwing the blob on, I would go ahead and change the color of it, and I like using the color presets. You can use the fill color and all the different colors on the rainbow, but I personally like using color presets. It's really fast, and our illustrators have put a lot of time into matching contrast and what colors look good together, so I find that it's a little faster for me. What I'm going to do is I'm actually going to knock back, let me just move the canvas over here, I'm actually going to knock back the transparency of just the inside of the fill over here, just so that it's a little more clear. Maybe I'll make it more red, and I'll knock it back more so that you can see the background of the brain showing through your blob and onto your image. So, it really highlights that area without taking it away.

The structure of the brain over here. And yeah, if I wanted to, I can throw in a tumor so I can type in ‘tumor’. This is just standard icons like Jacqueline mentioned earlier in the session. Throw that on there maybe make that a bit smaller. Whether that's that or if you want to throw in like neurons on there you can go ahead and do that as well. Maybe instead of a tumor we want to throw in some pathways. Really cool and easy tools to do this, so why don't I show you how to do that? So we have this neuron one, this works really similar to all the other kinds of nodes that you can drag them around, a new white one's going to appear, and you can keep infinitely dragging this around to make a very detailed version of your track. And then maybe I'll throw in one more neuron here, and I'm actually going to flip it using this little button over here so that it's tail to head and not just head to head of my neurons. And there you go, and a matter of seconds I've kind of created the brain. I've created like highlighting regions where it's more active and then the tracks that go along with it. And I do want to note that all our arrows are under the insert line so anything from lines to these neurons all behave very similarly in that you can just drag them out, drag out their nodes. I think someone had a question from the audience earlier of changing the width of these which you can definitely do as well. So yeah, just wanted to highlight that really quickly while we're touching on these neurons and these customization tools.

Cool, so we have that, so we have the brain, we have all of this, and then we have the blob tool. That's just one use case, another use case I would say is like making your own protein. So this just kind of looks like a Jelly Bean or a little kidney bean, but if you add in a DNA on top of it, it basically becomes a protein, maybe even a CRISPR protein. And say you made a mutation in the protein and maybe this little concave area, you made it more concave, you can go ahead and use the blob tool to go and manipulate that. So whether you made a mutation to make it a little more concave than this, leave your site and go ahead and do that. That's another example of where you can use this funny looking shape to really tell your story and your illustrations.

All right, and I just have a few use case examples here as well that I wanted to highlight. Some of our illustrators have done it before, it looks really complicated, but essentially it's just the brain stem and a cross section of the brain. I believe in the basal ganglia, and all of these are just literally those tools that I showed you that you can edit and drag the nodes around to edit.

Custom Lines

Next feature I wanted to highlight with circular arrows just because I've seen a lot of people make cycles in BioRender and I feel like this is a really underappreciated feature. One of my favorite features actually is this because why don't I make it bigger so you can see it better, but essentially it's just an arrow that goes in a full circle. It auto aligns automatically every time. You can actually go ahead and put your cursor over this white node, and if you take a look, it turns into a scissor icon and you can actually cut it at different areas and drag it around. So really, really great for making like cycles. Another example of it is like for plasma maps if you need to make these like gene maps over here, really great for that and I'll show you how to do that really quickly. Maybe we'll just thicken this up a little, add in these arrows, I usually find that plasmid map arrows are smaller heads so I'm just going to shrink that. I'm going to cut it into different parts for Gene A so I'll cut Gene A really quickly, I'll cut Gene B as well, Gene C, I'll make it a little smaller over here. This tool takes a little more getting used to, but I promise once you get the hang of it, it's super, super easy to use. We have our kind of plasmid map here. Why don't I go ahead and match the colors as well? Just as a side tip, if you're labeling something, matching colors to the label is actually super helpful in helping your audience understand the feature and what we're talking about. See over here, maybe I'll make this more of a yellow tone. It seems like my computer is lagging a little bit, so why don't I go ahead and just do this a little quicker over here. And just in a matter of seconds, you're able to make that gene plasmid map. You can show it in the context of an Eppendorf tube. A few more examples of where these like circular arrows come into play and I find that they are pretty useful for things like these phase diagrams or phase cycles for projects. Essentially, these are just circular arrows that have been designed in a cool way. So these are just sectioned off circular arrows if you can see here that the head it was kind of thickened and the head is gotten rid of over here as well. This cycle for the project cycle is essentially one big arrow that's been cut up in like text boxes are just put around it. So these ones that look really cool but kind of difficult to make, if you break it down, it's actually very simple. It's those circular arrows that are just put together. I saw this one where our illustrator is made, I thought it looked really cool, it looks really complicated, but essentially if you do need to make cycles like this, it's three. This is actually just like three big circles. These circular areas, if you can see one, two, and if you can spot the third one, it's this little one over here, this third one over here, and essentially it's just three circular arrows that were cut apart and there's icons in between them. So a lot of these really complicated looking processes too, if you know how to use the tool, you can just break it down, add in the icons, and I think you're at a good place to start creating those cycles.

Connector Lines

All right, so let me know if you have any questions about that. It seems like everyone is saying it's pretty clear on your end, but happy to go over anything and stick around for questions at the end as well. But I did want to highlight the last 15 minutes on really introducing and highlighting new features and two that I handpicked that I was specifically excited for, again with the concept of saving time and on the concept of customization. The first thing I wanted to highlight was actually connector lines. This is a feature that I've been waiting for a long time for us to launch and I'm really excited that we did. So remember the arrows that we just went through of how to use that? We actually have new versions of these arrows where you can connect it together and the really cool use cases like this where maybe I want to move the arrow to make protein A point to protein B, it is pretty simple. I didn't know it could get any better but we have made it so that we've made these connector lines so you can actually pull up arrows now and if you hover over any of our boxes they have these nodes over here now, you can see that. I'll zoom in a little bit too so you can see this node and it turns blue and I can connect one note to another node so it kind of snaps into place here. You can connect it here or I can connect it here. I'm going to connect it here because this is the diagram I'm trying to make and it seems like this is pointing to the left side of the box so I'm just connecting the bottom to the left side of protein B so protein A bottom to protein B is what I'm doing and this allows it to just drag around wherever it goes. I don't have to switch the arrow and the boxes separately, it just auto drags around. Really, really cool. So that if I wanted to change the placement here I can just do that and all I have to do is make this little Bend and there you go. That's how connector lines work. A lot less steps to get to where we wanted to do with this.

I also want to highlight that these arrows are not just for text boxes, they actually hook onto our icons as well. So this example, the petri dish, if I wanted to move this over instead of moving the icon and then all the arrows and then be like ah never mind I want to move it back, saves a lot of time just moving the main things and then your arrows just follow you automatically so really great for processes protocols things like these workflows.

Actually, one design tip I have as well: when you're making these complicated diagrams with a lot of arrows I would try to limit the number of angles going out from your boxes. For example, like in this case instead of having this angle going out from this label to this label maybe just making it a right angle would be easier. So if I wanted to shift this and make this a right angle I have to move the arrow separately like this whereas if this is connected I can just move it right along like this automatically and the arrow just follows so that's the big difference. I kind of made it so that the left side of this isn't connected and the right side is. So for example, say you want to shift all the labels down slightly I would have to switch the arrows here, drag out this arrow, and then drag this one down whereas this one if I wanted to shift this label and maybe processing details down I can just shift it down, the arrows automatically follow me up and down and there you go.

So that's our connector lines which I thought was a really, really cool another example in this kind of pathway is that again keeping in line with like limiting the number of angles that are branching out from your icons if I wanted to make this more of a right angle and I need to change this I would have had to like move this individually one by one and all the arrows to follow whereas in this case because it's used with our conductor lines I can just drag it right in and decide yeah I do want to make it a right angle because I remember the tip about limiting angles in your images and there you go it's a lot faster so that's another use case where this is kind of the before this is the after right angles look better so if you want to switch it up and use connector lines to make it easier go ahead and do that. I hope that the future is clear.

Custom Colors

The next tip I wanted to go through actually was customization and this is a feature that I think everyone was really excited for on the team to launch. I was really excited because I've seen some people in the audience as well talk about this feature and it's actually customizing the color in which our icons are offered. So things like this one, this is just a c.elegan, I can go into edit and I know for those of you who've used BioRender in the past you're probably used to all these like color presets which are really beautiful Jacqueline has covered in previous in her previous session as well but you can change the color like this but we can also do color overlays now which allows you to have like a more wide range of colors, almost unlimited a range of colors that you can do. So why don't I go ahead and show you if I wanted to make the c.elegan I like a turquoise color I can actually drag this scale around and make it any shade of this possible. Maybe I want to make it a specific branded color I can type in the actual hex code so I have the hex go for BioRender blue in front of me just because a plug that we're at a BioRender event so I'm gonna go ahead and type that in, maybe it's a branding that you want it could be your company branding, it could be your school's branding as well and that's basically how you would change that and that's just over available here on color overlay. You click on this little plus sign and then you can pick any color you want, type in the hex code, depending on your brand or depending on your school logo. Maybe it's just your favorite color. You can go ahead and do that.

A few more editors that are available here now you can make it transparent, the saturation is something that you weren't able to edit before but now you can so if you want to make it a little less that saturated meaning like less color pigments to more you can go ahead and do that over here with the slider. This is a really cool feature that I'll highlight in the next slide which is glow which is really good for luminescence and GFPs and things like that. I wanted to highlight this mouse because while playing around with it I realized that we can actually now change individual aspects of icons as well. So for example, previously you were kind of used to this like color piece, that's again maybe I want to make this like a brown mouse. I can go ahead and do that but now you can actually select the flesh and the fur and the eye separately. So what I mean by that, really, really cool, the flesh over here I'm selecting that refers to all the skin here so if I wanted to make it red versus purple or even like this green color I can do that it's really, really cool. Maybe I'll make it like a purplish pink over here I can do that. Yeah, maybe I'll make it Pink for now and I'll apply that, super cool right? And then the eyes as well, I don't know if anyone's noticed, I just figured this out yesterday but if I click on some of these icons and I click on the eye I can change the eye color as well as if I wanted to make it red versus blue versus like green glowing I can do that as well so really, really cool.

As well, this is like one of the customization features that I thought was exciting and you can click on all the different layers just by selecting it here. One example of the glowing feature I actually wanted to highlight was if you have an example of let's say like a virus or protein and you want to make sure that you know the outer things are glowing or it's a GFP. poly will actually highlight like commenting as well in the next feature but over here for example if your Pi was like make these fluorescent uh green and then they actually gave me like a hex code to go with it um I can just go ahead and select all of these proteins together uh maybe make it that green color that I wanted to by just typing that in over here. I'm just going to select the screen for now, and then maybe just play around with the saturation a bit. If you can actually go to this glow, you can make it a glowing protein over here which I thought was super cool. It's the weather. You know, the glowing is activated or deactivated in your image. You can just go ahead and change that up here and how strongly it's activated there so that was I thought a cool feature that we added as well that I also wanted to highlight.

Awesome, and last tip I had, it's kind of cheesy, but it was just to remember to have fun. Our team internally has a lot of fun like thinking of all these features and building them out for you and working with the community such as yourselves to create a lot of these features. So, I just want to make sure that everyone knows of all the different features and make sure you have fun with that as well. 

That was my last tip but yeah just remember to have fun, enjoy yourself on BioRender as well, and I wanted to say thank you for joining me and thank you for joining the session.