How to MASSIVELY enhance clarity in your science figures

okay thanks for that Simon I'll just quickly redo this all right thanks brick you know I just wanted to kind of do a quick overview seminar on how to make scientific figures and really kind of just go into depth on how the process of taking figures you already have and improving them as well as maybe go over some other items that could be useful for folks and with that let's get started so as I was mentioning first time around I want to just briefly touch on software and tools to use for making figures go through some step-by-step examples for improving existing figures kind of talk about the thought process and the design process of designing a figure and if we have time I can go through some demos and ask some questions it's pretty much up to all of you what you think will be useful and kind of get things started I guess the first thing to really ask is so why should you care about figures in your scientific work and there's there's really a lot of reasons I'd say one that one of the first things is that figures are usually when the first items someone will look at when they're looking at a manuscript usually you see the title see if it's something that's useful for you you might browse through the abstract at least for me I think for a lot of people you'll you'll browse the figures and you'll see okay is this is there data in here that looks relevant or useful for me or is this something that looks interesting that I wants to know more about and having good figures are really important and effectively conveying information and really as a scientist we're trying to one discover new things but we're trying to discover new things so we can share it with the rest of the science of the community and if you can't effectively do that then you're you're lowering the impact of your of your work so really you want to have you want to have good science but you also want to be able to communicate it effectively and if you're curious about what bad figures look like there's a in this in this PowerPoint down here I'll send this out later and there's kind of a graph on the side I was googling and so what is the top 10 worst graphs and there's a this figure comes up a lot in these articles and is basically this complicated 3d I guess bar histogram chart which you can't actually see one what color is really what in here you can't see the differences that's trying to be explained there's no figure cache there's no labels on any of the axes there's a lot of things wrong with this so let's try it not to do that so really kind of backing off too so what what is a figure comprised of so here's an example figure out of a paper from our lab this was published in Science Translational Medicine and there's there's a few components of the figure there is usually maybe some schematics and so the purpose of the schematics are to convey concepts or processes that are difficult to explain with just just words so you it's there to add a kind of visualization to help guide the guide the reader and there's usually some data and the purpose of the data is to show proof of your findings to really reinforce what are the conclusions you made from your from your experiments your simulations whatever you you determine and lastly there is there's a figure caption and this is also a very important point so the the figure caption should provide any detail that is message that is necessary to understand the figure and you're not going to be able to do it a hundred percent you're not gonna but you should always kind of strive to have a have a figure caption that is that is short and concise but can also explain to someone just just reading and skimming through what's going on and then within that I you're gonna want to usually you want to have a first sentence that just summarizes the entire figure so the idea is you're you're really starting from like summarizing this is what this figure does and then in the following sentences you're gonna talk through and concise points what you're trying to convey with with this figure and so like for example in this figure right here we're talking about using a microfluidic chip in order to look at the deformative deformity of cells taken from patients and seeing if how these cells deform and flow correlates to whether it's cancerous or not great so if you want to actually go about making making your own figures what type of software can you use so typically people for plotting data at least people like to use Excel there's things like Origen MATLAB Python there's our there's really a ton of different toolboxes you can use to plot things and honestly it doesn't matter what you use as long as you can use it to convey the information in what can be I personally prefer using MATLAB for most of my data plots that's I'm familiar with it I do a lot of my analysis in MATLAB I know a lot of other people use it sometimes Excel is easier for doing things really quickly but you just really want to be familiar with whatever whatever software that you're using but really you can make any good figures with it with any software if you spend enough time really just kind of learning it and getting a feel for it in terms of making schematics I personally prefer to do mostly 2d schematics you can do these in PowerPoint really simple so if you're doing something really quick there's more kind of slightly complex software like Adobe Illustrator CorelDraw and Inkscape in terms of so for me I I use PowerPoint if I need to do something really quick it's pretty intuitive to use they have lost shapes filled in but for most of my figures I actually use Inkscape which is a a free kind of professional ish grade vector graphic software it takes a little bit of time to get used to it but when you do become proficient with it you're able to make pretty nice figures relatively easily in terms of 3d I actually stay away from 3d as much as possible because it tends to take a lot of time some people are good with it and can get some nice figures out of it blender is a free software people use a lot OTO Autodesk has things like inventor there's SolidWorks is another program I think Simon here is use SolidWorks a bit making some 3d graphics and autodesk is another one fusion 360 this one actually like because it's I've used it a little bit it's free it seems pretty intuitive blender has a program for doing 3d stuff it's powerful but it's really difficult to use so I don't tend to I never really kind of got hooked on it but some people use it and that works for them but I I mostly stick with this with the 2d you really want to avoid over complicating things if you don't need to so if you can convey most of your information with a simple 2d schematic that looks somewhat nice I think that's that'll do 90% for you what about paint yeah so there's some software that you might be thinking of that I did not mention at all and this kind of segues into my next point of so vector images versus bitmap images so a vector image is a is a image file that is all the information is conveyed in you can think of it as like almost like equations or a mathematical representation of lines and gradients in other shapes so it's not whereas a bitmap is literally just if we had a kind of a gridded sheet we would assign colors to each each square and so wouldn't you see the difference you see in these is usually when you're when you zooming in or when you're when you're transferring data between different software if you if you magnify a vector image no matter how far you zoom in you'll still have crisp lines whereas a bitmap you'll lose reservation as you as you zoom in so generally vector images are nice for making schematics there's nice for handling data because if you ever need to adjust anything you're always going to preserve the quality as well as all the all the information there so bitmap so Photoshop paint all software that people used to make these types of images I usually don't I won't use these for any and a scientific figures vector graphics so illustrator Inkscape powerpoints and the other ones I mentioned on the other previous slide these are all great they have there's different vector formats so so bitmap format so TIFF JPEG PNG BMP these are examples you use these with images because images are always going to have to be a bitmap so you will have to use these for for some for some parts of your of your figures but if you're making plots if you're making illustrations these file formats are definitely ways to help preserve the quality this question yeah Hamish so so I I understand why vector graphics are better right but the thing is when you you make them in Illustrator or in scape or whatever after that you have to transfer it into a word document or something right when you are putting together your figures right so how do you how do you go about that what do you do there yeah so there's a yeah it's a so-so EMF and WMF are formats that are vector formats that are compatible with word some things so for example these these formats they can't handle transparencies so sometimes when you if you're working in one program and switch it to other there's certain details that might get lost I know if you're using word on a on a Mac you can actually save it as a PDF which PDFs are also they save as work they can save it as vector formats now if you're using law tech or other approaches to kind of craft your documents these also handled these format files so sometimes it is not annoying sometimes it can be annoying trying to get the the formatting properly and it really just depends on which which hardware software you're working with okay thanks great Inkscape is free I guess one caveat and I guess I think fish can attest to this is that the current version of Inkscape the Mac compatibility is not that great illustrator definitely works well it is not a free program but it works fairly well power PowerPoint is actually a you can make quite nice schematics in PowerPoint if you spend enough time working with it I've seen some pretty impressive things out of at a PowerPoint yeah actually even on a Mac it downloads it so that you will run it in a Windows simulator so that's kind of why it's like really laggy it's pretty terrible to use yeah and I'm not sure if so they release the latest version which might do it actually in the native Mac kind of software it but I'm not sure I think Dan tried it didn't work that great I think yeah so I guess that the point trying to make is there a lot of different tools you should be aware of these things find what works best for you but it really doesn't you you can always make some you can make nice quality figures with really many of these different softwares so just figure out what works best for you so in terms of in terms of actually plotting so here's a here's an example of just a plot I constructed in that lab on the left is a tiff image on the right as an SVG so right now they seemed mostly comparable it's hard to see the difference if you zoom in you can see clearly with the TIFF image that it's a pixelated image you lose quality as you as you zoom in to this so if you're say for example you download a PDF of a paper and you want to kind of zoom in on some data points it would be blurred and you want to be able to see details whereas with the vector graphics no matter how far you zoom in and this also works with PowerPoint too so this is just I put the vector graphic in directly into into PowerPoint I was able to crop it and scale it and it still preserves the the image quality and I guess I can maybe bring up one of these examples but so there's also another advantage to using these vector formats and that's if for especially for plots is that it lets you when you're compiling your data you can actually edit a lot of these things in the software so say you generate a plot in MATLAB and you're kind of compiling a figure together and you're like oh I don't really like the font size that's associated with it you can actually if you're using a compatible like vector format software say like Inkscape you can actually edit a lot of the details in that software so font size the data point size the line widths these are all things that are they're editable because they're saved as like individual objects within the file instead of a kind of pixelated image and also some examples later on kind of going through that and how you can kind of change these things some-some tips really to kind of improving your your your plots I was going to kind of go through and it like an example a simple plot so so this is a default plot for MATLAB you can kinda understand what is being depicted here there's a there's three people from our lab key K Rob and myself it's describing how our sanity changes over time relative to how many days we're spending in lab it's a it's a plot that you can understand but it's also if you can imagine if you shrink this into a research article maybe it's a little bit harder to look at it's not aesthetically that pleasing the texts are kind of small the lions are hard to distinguish just by color from immediately there's some things that are not perfect about this figure and I'll kind of want to say as a rule of thumb if you see it if you have a plot and you can immediately tell which program that plot was used to make to make that data there are two plot that data then you probably didn't spend enough time formatting it so if you look at something like okay that's like default Excel format it really kind of 1 it doesn't is usually doesn't look that great - it kind of signals that you didn't spend that much time working on it and kind of crafting it - to a format that you think looks better and also conveys information better I can share this a bit later we have it on our git lab I need to update this but I have some default function or not default but I have functions that I've built in MATLAB that make it super trivial to to change the the plotting of the of your figures so if you take it from a default we have a function that I made called pub fig which is like a basically a function that makes publication figures and so when you run that and you can adjust some of these settings but the the main idea is it increases the font size so you can have a a plot that doesn't take up as much space but still is easy to kind of understand and see it changes direction of and size of the ticks and other things are up to preference to so you can adjust it to however format that you that you like for instance I don't like having the legend box so I remove that it also increases the the line thickness and I'm gonna open up and it's pretty easy to use so I'm opening up MATLAB right now so I just have a simple plot right here I'm just generating data see if it actually what come on okay so it looks something like this and then all you have to do differently in this case so I'm just gonna add a line that says Pub fig I have a function in my in my my folder so I it literally will just grab whatever the most recent figure is and then it'll just adjust it according to my specifications and if I go into here so this is I've been working on this since maybe like eight years now I've just been slowly updating I had like some matlab function software that got off from like the the MATLAB database that I had initially started with and I started editing over the time there's a lot of things here but there's some simple things where you can just change the defaults of the font if you want if you have like a specific size that you need of a figure one thing that's nice with the way I've coded this and I'll share this with everyone is if you say you don't like the size or the things you want to change the settings I also set it up if there's like an option that it'll bring up a where is it uh-huh great I'll bring up a menu here and you can inches so I was like okay I want to with three inches I like this aspect ratio want the font size to be smaller I want the marker size will ever know having using markers here I say I want the tick length to be a little bit shorter you can adjust all these things and it will automatically set it up for you and if you want to save it as a as a vector format see if you go here save as and you can have a location and then so EPS DMF PDF SVG these are all vector formats I usually save as SVG this is what's natively used in Inkscape but most of these formats will work great Joe yeah so in the in the options menu that he just pulled up for pump fake width is what is the width of the final figure yeah I think it's the outer box it's not exactly something most of my editing in Inkscape if I need to adjust the size at least lets me get close yeah so you can edit like you can say the final outer box I wanted three inches or two or whatever yeah if you want to sometimes it's and you have to kind of scale down the sizes right right this would be like a taller one that's even smaller okay you can kind of get a sense to what it look like when you're trying to fit a a graph into a small section of a but yeah of your paper I think I think that's quite neat because a lot of times that's what I do struggle with because I have my figure but then that is at some size but then when I put it on word it needs to fit in with like all the other figures all the other data and charts within the same figure right one thing that's nice too is that even if it doesn't get you to the exact size you want it makes it easier to normalize your plot size between between different plots if you have like five different plots and you because otherwise right a lot of times people like okay I'll just spread this out until I get to the size I want but if you do that then it's if you have multiple plots it's hard to keep them the same and you can I mean you can always program directly in MATLAB to make it a certain size it just takes a lot more effort for the for the editing so I think like changing this for example this figure from the default would probably have maybe like 20 lines of more code they'd have to write and so it's kind of a pain to have to just write it over and over again go back here great kind of back where we were before so here's a fake eerie and kind of the next thing I wanted to bring up is okay so this is this is alright to distinguish it's not like a perfect figure but really when you're plotting you need to think about to how how you want to plot your data what makes sense so here I'm drawing lions but maybe this isn't is this a continuous data set is it is a simulation or is it experimental data is it a survey for example so if it's an experiment where you're say surveying at different days for multiple people and then you're taking an average of of that maybe that survey this doesn't represent all of that information so in that case you might want to have distinct data points for each of those different time points you want to include error bars which usually you're conveying standard deviation so this is giving you one it's giving you more information about kind of how the experiment or the was performed or which data was collected and it's also a lot more transparent so there's there's more information being delivered in this case and so I usually like for my workflow at least I'll kind of take this mostly finished image and then I'll do my final touches when I'm kind of compiling so and it depends on the journals too and I'll go into a little more but at least for a lot of journals that we submit to it's usually not just one fly it's usually a few plots kind of compiled together that have one one overall message for the for the figure but for this for example if you wanted to kind of touch it up a little more you can think of ways how to better engage the information that's being conveyed so for example right here I'm trying to convey information about three different people in our lab maybe that's not immediately obvious unless you know who this is so one modification you could do is say put the figure put images of the people inside the plot and have it color coded to whatever data is correlated with it this is all can be done in an Inca here for example I did some other slight touches too so if you have colors in your plot so you might as well use them to kind of convey additional information so here in this case we're talking about someone's mental state of being but their their quote-unquote sanity so here I'm using kind of blue colors to convey someone who's maybe has maybe more stable emotionally and then for myself down here I'm using maybe warmer colors that are conveyed kind of the opposite the opposite feeling and I mean this is like kind of a very random example but there's there's definitely ways when you're depending on what your experiments or what you're trying to convey there's you should really think about how all these deep tails are conveying information to to people even if it's like not as obvious and more on a subconscious level it's looking out and yeah I think and so if you're curious what it looks like let me see if I can open up all right so this is Inkscape right here the compared to illustrator I think it's a lot more simple and I can kind of go through some examples later but there's like really like simple shapes that you can make with it and there's tricks to do like pretty like nice-looking geometries or things pretty easily you can change the colors pretty easily you can make gradients if you want to make gradients but when you when you drag a plot say from MATLAB if it's saved appropriately in here you can actually go in and adjust things like the font size so I can make this larger if I want you can actually say you don't like the line thickness you can actually go here and adjust the line thickness to make it thinner or thicker or in my case I actually went through and I changed the color of some of these these plots how I sauce it and so it's nice cuz it makes it easier to kind of play around with it if you're trying to instead of having to manually type in and change or click on a bunch of things and the other plotting software to get it to the format you like and then you can kind of group things in this case I just have kind of drew a box around this so it's nice for especially and I kind of go over it in the next example when you're trying to construct a lot of elements there's conveniences of having like one kind of interface that you're working with and you can do similar things in PowerPoint to especially if you're working from Excel into into PowerPoint and so it's it's not just unique to this to this program so Joe yeah you said if the file format is appropriate you can like edit it on xscape right great okay so for every vector format or the one that you mentioned you can do pretty much in any vector format so some of them it'll like import but usually it's pretty good about it so SVG you tend to not have any conversion issues I've used EMF I've used PDFs before I'm is usually pretty good about handling it okay thanks yeah I have a question about the images that you use here because I can see all the other elements in this are definitely vector elements but it's raised to me like it's an odd mix where you actually have images in there do you know how's that handled I've been really I've used Inkscape before but I haven't really seen that functionality yeah so you can anything that's not vectorized it just raster it rasterizes it and you can do that in the form and the file format lets you do that lets you have a combination of the two it's just that obviously it's not gonna be preserved if you if you zoom it like you're gonna lose some quality at some point right but it it the the file formats are usually meant to be able to handle handle both you can have some issues when they're confined and you're trying to get it to you know there's some importing exporting things when you're working with word where it's usually not that great at dealing with this but uh things like late actually are really great I handle a in these these these formats so if you're using what's the one that everyone uses I just forget overly fuel is pill relief it should work fine I think great so I think kind of going on here so this is where we kind of started with this is what our final figured looked at that we ended up with and you can see that just like immediately it's it's one we're conveying our data more properly it's kind of easy to see what these these data's are correlating to if you you can this is made large right now but you can imagine this could be a half column figure and really easily be read and understood another point I wanted to bring up is that you should put some thought and so the colors are using when you're when you're formatting things especially if actually there's a lot of people who are kind of working like apply math or physics well some of those journals still do black and white or black and white is common so you should if you are including color and plan the habit you should you should think of how it looks on the grayscale as well as in color and it's also good to think about how say for example like different color maps how they will be distinguished if it's one of its grayscale but also too if you're if you're someone who's colorblind and can't actually distinguish the color spectrum as well so let's just say this a plot that just shows what different color maps look like for different types of colorblindness and you see ones that like it works it's not it's not the greatest I think this doesn't include perilla is like the new MATLAB color map that is it was designed to be very distinguishable even if it's someone who's like colorblind and so you see a lot of these programs are kind of updating to accommodate for that for that now so it's just something to keep in mind can you take like a simple plot like this and RGB it's actually pretty distinguishable still if you have some weak colorblindness but in grayscale you can imagine that these are terribly difficult to actually distinguish like which one correlates to width this one's obviously lighter but then these ones aren't as obvious and this is also something you can fix by just adding markers that have different shapes or by using different styles of dashed lines there's just something to think about when you're kind of formatting things if we go back to my other example we can kind of see here that on grayscale we're able to distinguish these things one because the markers are different we have triangles we have squares we have circles the shades are all distinguishable enough from each other if I was to actually edit something one thing right now is it's not clear which one of these marker shapes actually goes with my my picture legend so that's something that could be improved slightly but at least that the colors are distinguishable um so this is just kind of I just did an overview of how to kind of kind of rationale through like a single figure I wanted to kind of discuss now about how you would compose a entire figure that maybe includes multiple components so either schematics include data includes some experimental images and so I just kind of want to go through like the process with an example feel free to stop Joe before you get into that just relating to the earlier point even on so on photo sorry illustrator there is an option when you go into like view there is a way where it'll show you what someone with a particular kind of colorblindness will see your figure as so as we change so you can also preview your figures that way yeah I forgot that that's does a great point I forgot to bring it up yes so for these ones for example I was it in Inkscape they have a similar thing if you go to like the tool box and go to filters color and then color blindness they have options for like these different types of color blindness so you can kind of preview it and I think I'm sure PowerPoint has similar things or you can at least do grayscale pretty easily yeah thanks for bringing that up cool so kind of going through this first thing so one obviously keep your keep your audience in mind right is this a is a very general audience are you gonna have to convey more simple concepts first even like get the idea across or is it a very specific audience that is like already very technically aware of the subject you're gonna be discussing one thing you could do is look at journals that you would potentially submit to and see what other people have done and this one gives you an idea of maybe what type of style that that journal prefers or how people normally convey information in that journal this is also useful if say an editor is looking at their paper if they if it if it looks similar to like something that they normally publish into their journal there may be more willing to kind of on a subconscious level even give it a give it a chance but you can always like there's there's always good examples and bad examples too so just like keep a mindful eye on to what people are doing well and what people are doing bad and there's definitely different styles that kind of emerged in a lot of these different journals here are some some examples so this is a paper from our lab in PNAS it's a kind of experimental slash kind of theory based paper it includes multiple components includes a schematic up here it includes some experimental images it includes some more experimental images down here and it's I'd say aesthetically pleasing it's a it's using kind of colors in a way that allows you to kind of correlate some of these things this is like intended more for a general audience this is a paper from PRL so this is more of a physics focused journal I think probably at the time they weren't even using color so everything's in grayscale it's very kind of practical into the point like here are the dimensions here's the details here's the data here's the experimental image and this is an example from our lab pretty recently so this was published at Nature biomedical engineering so this is like a very broad audience scientific journal so it's it's targeting it's it's you can see here like they're they really looking for a very clean aesthetic so having these like really polished figures that have like nice schematics and just look very appealing because they want to kind of be able to highlight that when they're when they're publishing their their journal so just something to keep in mind even before you start start working on working on making your figures in terms of actually composing so first step just you want to determine what you want so actually conveying your figure really because your your figure the whole purpose of it is to convey information so you want to have a clear idea of what you're trying to do what what's the objective right so here I'm going through an example from one of my papers so my objective was to create a schematic that showed a process in this case we should have made a process to make hydrogen particles and high throughput and use them for tissue engineering applications and maybe I have some some points that I want to address so I want to make sure people get an idea of what the device looks like I want them to stay able to see how the droplets or the micro gels are actually made and what I'm actually using them for in the in the paper and and then I'm keeping in mind too that this so this is more geared towards a material science and engineering focus journal so and those ones I know that they tend to have like these maybe larger figures with some may be cleaner illustrations and showing and a lot of experimental images as well mixed in with schematics and here's the citation but so so once you have an idea of what you want to kind of convey in the figure next step is just sketch a rough draft so just kind of playing around on paper you can also do it on your computer but here's an example for mine so I was just kind of sketching out like okay maybe I'll include a schematic of my device here just writing in like all included image of this I'll have some schematic of that and put some other things here and so I'm kind of just framing it to how I would envision it show up in so and sometimes you'll want to edit this too and it helps you kind of frame a nice tight illustration and figure so next up once you start getting data you can start actually compiling this and so this is actually after quite a few steps but this was an intermediate version of the of the figure so here we have our schematic illustration of this device that we built we're injecting some polymer solutions in we're using oil and surfactant as a way to create these uniform drops in this device I'm kind of going over briefly what the mechanism is for how we go from a droplet to a gel and then I'm showing here how we're actually using that so in this case we're using them as a way to make these kind of beaded scaffolds that allow cells to grow and proliferate and but even with this for example like so there's some things I'll point out that I don't quite like with this figure so for example here the scale bar is a little small so it's kind of hard to read over here this step is maybe I had some feedback that this step was not really clear how exactly this was done they're just kind of like in your imagination so here's the come after kind of revising some of these things here's a final figure and there's also a lot of other differences too so we actually redesign the device we did some other things but really just kind of editing this over time so so the scale bar is a little easier to read here we actually change the polymers we're using a little bit this step I included a schematic to try and make it a little more clear how exactly we're doing these steps and then this was the kind of finalized figure for that and I think I can pull it up on one sec let me open it in oh here we go so this is what the figure looks like and this is loading up right now um I'm a question in the meantime then so how do you decide like what sections of the figure to make the different some figures like a B and C in this case yeah so like wick like topically what to include yeah yeah so I think for this for example I had a clear I had a clear workflow that I wanted to describe so if it's a workflow for example it's maybe a little simpler because you're just going kind of chronological so to convey my workflow I need the first step is we generate drops the second step is we cross link them the third step is well we do some stuff in between but then we but then we use them for our application if it's maybe [Music] yeah I think in general I but I think yeah you're getting planet in general so if for example if you're just if you're just trying to explain some data right if you have some data that you're trying to explain a result with it would usually make sense to include the schematic before the data if the schematic helps you envision what the data is trying to show so if the data comes first then you see that that's the first thing you're gonna look at and so if you if you need something farther down to understand prior that doesn't make sense so it's usually want to configure it in a way where it's just like reading a reading a sentence reading a page it's an order that makes sense to understand it chronologically and there's there some tricks with that too so here yeah we have I have experimental images that are included in kind of this larger format what one thing I like to do at least what this is all I'll create a word page that is the size of an actual page of paper and then I sent I set these guidelines to the boundary so I actually can make the figure to the appropriate size so if you're doing like maybe a half column figure you want to include it in the space here and then this also lets me kind of format the the font size to something I know that'll be legible when it's actually put into the into the manuscript so here I'm kind of being generous I'm using size 11 font for these kind of sub sub sections of the figure for some of the less important things you can afford to be smaller you can do like size 8 I think down to usually 7 is probably the lowest you'd want to go maybe for like the tick marks on on the plot or something and so yeah it's nice with this because it lets you kind of real like kind of play around with all the components all at once and rearrange things as you need and there's also tools to say if you want to make these aligned it'll align them set up you'll kind of notice that I definitely with these I pay attention to how everything lines up so things line up well it's usually more appealing to look at so if I if I offset this like a little bit I just kind of look a little bit strange just someone kind of looking at this so you'll notice that like a lot of these sections I try and line up as as best as possible sometimes you can and that's fine and I guess also to to try and kind of highlight how so some of these like so for example this I actually made in Inkscape so this was not like a 3d rendering or anything these these particles I just literally combined different circles with different gradients together so I kind of create this 3d looking effect or a transparent 3d looking effect this I don't know if I'd recommend doing this necessarily but to construct this kind of 3d 3 I actually just did a bunch of kind of perspective lines and then actually constructed it in here piece by piece so you can actually go through and break this apart and it's just like a bunch of different components that I compiled so she's like a lot of squares lines and gradients and things this took a little bit longer I realized after actually I was going to show another example so actually so for this this paper we actually got the did the cover art for it let me see if I find it so this was the cover art we made so I actually made this in Inkscape and if I actually open that up is I mean this is clearly more advanced but it's one I like highlight that you can even just taking like simple shapes and then if you know how to kind of compile them together you can make pretty nice-looking images and so this is just and you can kind of see here oops viewing layers so I in this case I kind of set up a bunch of different layers to make it easier to follow what's going on but uh yeah so if you if you get familiar with these systems you actually make these pretty elaborate illustrations so this I did not actually draw at all and in here because that would be oh that would be that would be painful so what I did do which I found was a nice trick is that you can actually take a 3d like AutoCAD it's like a any type of modeling software you can create a see if I can find get it to open open you can export it as like a PDF and then so I did that with like a AutoCAD design and then I imported it into Inkscape and it converts it to the vector format cos PDF and so I was able to just kind of click on all these and had bad lines I had gradients well let me do it but might get angry at me because it's kind of a large file but uh too many layers actually and just to kind of highlight that you don't need to even use like this fancy of a software too so we actually had a so ream in our lab so this was a cover art she actually made that got onto lab on chip and so this was actually made in PowerPoint and I didn't believe her at first but then as I looked closer I realized okay maybe yeah this could actually be done I think she exported maybe this out of MATLAB but just using just using PowerPoint to make graphics she was able to get it she actually got the I think the front cover of the the journal for this for this article which I thought was pretty cool and impressive and so I think kind of tying in that point like as long as you have like a nice vision for these things it really doesn't matter which tools you're using as long as you use them well and kind of think think through the process and just kind of touching up on these notes if you make it through here great so just kind of some some final thoughts like really this is an iterative process so like don't be afraid you don't have to get it right the first time it's best to just really sketch things through and iterate and iterate and you'll kind of improve over time and if you're gonna spend time making figures make sure you prioritize ones that are useful so sometimes you can fall into a trap of spending a lot of time formatting something or like trying to plot data a perfect way and if it's just gonna be used one time in a presentation or maybe it'll get put into supplemental information of a manuscript maybe a song is worth spending that much time on unless maybe you want to practice but it's definitely good to prioritize things that are maybe more will eventually get put as like a main figure in a presentation or sorry in a manuscript and yeah try not to you don't have to over complicate things too I mean so that's why it's good to from the beginning really construct what you want to convey in a figure and have an outline of the the main message you want to make and this helps you kind of focus your attention to really making something that's concise that conveys the information you want to to convey without having too much like say you don't want to have too complicated of a design that maybe distracts the reader from the actual data that you're trying to share so there's just something to keep in mind and I think the the small details although they're not as noticeable to maybe mm to every people don't immediately notice them unless they pay attention to these things but they're also you notice them subconsciously so things like how figures align the font size the colors used all of these small details although they get neglected I think they're important for crafting something that that looks great and will have your your readers or your audience really kind of appreciate the work more so on that note if you have questions I think we're running out of time now anyways I can go through some other things if you want but on that note all and my presentation okay thanks so in our meeting yesterday you had those figures or there's like little figures of the spheres kind of mushing into each other oh yeah so like I'm just wondering it seems like they match the photos pretty well how do you actually create those and like make things that match photos or like microscope images yeah I think I maybe part of that is practice I don't know if I have an example here I can open up a new document - nice thing with a lot of things that we work with is that they're very simple shapes so you can actually get pretty nice I don't think I need the grid you can make pretty nice things pretty quickly just by like just kind of knowing some small in this case setting so if just like editing may be some slight gradients here or doing masking or something so here if I maybe I'm making a great hydrogel or something I don't know I don't really like this color but or I say with maybe a little more transparency maybe a little color something like that but you can also like yeah I think simple shapes are pretty easy to make and it's nice because you can just copy and paste them too but yeah I think like for that for example I I know what you're talking about for that for example like I think had two spheres next to each other that were deforming so I think I set them up so that they lips just had them aligned had them touching and I wanted to show deformation so right now it's a circle but I could do is say convert it to like a there's a lot of tricks with all these software's but they clearly do this and like incrementally change some some part of it and so in like this case I have like two particles that are pushing into each other and slightly which one am I looking for I think it's this one no I'm gonna get this there we go yeah I honestly I just like you can you can always put the image in it too and kind of adjust it to get it to the the exact shape you want or you can actually so depending on what you're trying to do as well you can you could always trace it you can always import it and then and then trace the object to there's some other interesting things you can do as well where if you say you have you can actually see object okay so this was like a larger image that actually clip you can actually like go in and maybe I'm gonna do a really quick version but you can actually like go in and have a very detailed crop say if you want to extract parts of image things lips so here's a line that I made make it literally just go like Boop and clip it out and do like simple edits and things like that sorry did that answer your question yeah yeah thanks yeah yeah Jong sorry did you have yeah so it seems like when you make your figures you have all the was it sub labels like ABC together into figure right do you have ideas how to make like each like self figure individually and like some ways that you would because I use latex overleaf that means like usually you would have some figures and each figure is itself like how would so my my question might be like so I have like say you have the three sub figures right now right individually like how would you organize they're like size so that like when you plot it put it on over leaf they would like much nicely so I guess so for overly you can actually compile multiple sub figures is what you're saying correct yep and do you need to do that in order to have it have a unique identifier or could you just if you say this is a PDF could you just input you can't do that but like one thing you want a no release that you do is you label your sub figures and you refer them like later right so if you don't have that you have to every time you like refer a figure you have to like say like figure this is figure five then you have to like figure five and a and sometimes maybe if you change the figure it won't automatically change so you have to search for all the figures which is a little bit more yeah that's I can see how that'd be annoying I think well at the very least you can always have it refer to the the the single thing a single thing if you move the sub figures around then obviously you'd have to to change it I know I yeah I guess it depends on how how frequently you would change the ordering of these I do what I do understand what you're you're saying there might be some so and overleaf you can like in later you can actually decide like your size of yourself figure okay but I'm not sure how that will like how you would incorporating escapes so that that will yeah I guess if you so the one option is you just you compile the you just compiled the whole figure and then you have to yeah unfortunately there might be I would be checked there might be some workarounds for that although you still have to manually update the sub figure references yeah they also automatically assign some like margin between those figures that's also yeah but I mean yes I guess the only media workaround I can see is that you'd have to manually label 2 sub figures but you can easily put this whole entire figure in or if you have some design for like a another figure and I guess it really depends to like what you're more comfortable working with like you don't have to compile them I like to compile them in this because I add a lot of schematics for my for my for my things cuz I like having more flexibility with when I'm working instead of having to have three like multiple separate files and I'm trying to be scale just right and get it to fit in a perfect way but for something if you have like like maybe it's just by a schematic and a plot underneath or a figure underneath or image underneath it could be easier to do it to do it that way right where you're just coding in and overleaf and saying okay so figure one a insert this figure one B insert this okay thanks I think that helps great did anyone else have any questions and I'll put some of this information and I'll send an email people well okay I guess I'm not no I'm gonna and this session thanks for coming out I hope people found some parts of it helpful or useful if you have other questions I know I I love talking about these types of things that's why I like well I was excited to kind of give give this to this talk but yeah just let me know oh yeah so if you like you're presenting it to like in group meeting how much like effort would you put on your figures I don't I don't I don't try and put I I fall into the fallacy of spending too much time because I I like to just track myself with it I well the only thing too is that once you I guess it's also how much how comfortable you are with like Inkscape yeah yeah so like there's some things and I know I've like cuz I've helped other people kind of get kind of learn the software too and in the beginning it's always gonna be kind of slow and that's why some like things like PowerPoint or sometimes better for just doing like really quick things for presentations but like some once you get like quick at it and at least know the the kind of all the tools and stuff you can make pretty nice figures like pretty quickly so like I won't spend more than like 30 minutes making stuff for like a presentation or the other thing too is like you can imagine that once you have they're like they're like building blocks to so like once you have something made in here so say I want to I could easily take I think those go to sorry how is showing the wrong screen you can easily go to your you usually like take components of previous figures which I do a lot and I'll use the you could use these to kind of combine to make something else right so you don't have to make it again every time but or something like I do that along with some of the other projects we have a lot of these crescent-shaped particles and so like I'll put a cell on this one or I'll just change it to add this little thing so a lot most of the time I have 80% of the figure already made and it's just adding some adjustments okay it's actually it's a good point because once you you're kind of building up like a toolbox - and I know Dino does this lot to like it when he's applying to Grant's he just has like this one illustration of a cell that he's probably used for like 10 years you just spend a lot of time making it nice to begin with and then you can just give him this recycle it as you move forward or make small adjustments as you go okay thanks thanks Joe yeah thanks for Fair coming out everyone so that is the end of our figure making seminar if you would like to check out more videos like this or want to learn more about our work in the DeCarlo lab please check out our website see you next time

Channel: DiCarloLabUCLA

Views: 6,143

Keywords: figures, data, science, papers, school, education, ucla, biology, engineering, biotechnology

Id: 1XKHm8MJt1I

Length: 61min 23sec (3683 seconds)

Published: Sun Apr 19 2020