Illustrating Scientific Discoveries With Adobe Illustrator, Part 1

September 5, 2023

Question and Answer from Illustrating Scientific Discoveries With Adobe Illustrator, Part 1. This webinar took place on Wednesday, August 23, 2023. To view the on demand recording please visit https://neuronline.sfn.org/professional-development/illustrating-scientific-discoveries-with-adobe-illustrator

1. Can we use the smooth tool of the pencil even when we trace over a picture?

The smooth tool can be used on any line with more than two anchors. In practice, I have found the smooth tool to only be slightly useful because the effect it has on the line is somewhat unpredictable. I recommend using the direct selection tool to select the misplaced anchor and adjust it directly.

2. What format should the figure file be in to be able to modity the components in Illustrator?

.pdf and .ai files are editable in Adobe Illustrator. The degree to which you can edit a .pdf varies depending on how the original file was saved.

3. Wondering for instances when I’m using R, for example, instead of Matlab?

I am not familiar with R. With most programs that produce graphs, the window has a “Copy Figure” button in the menu. At the very least you can select the print option and select print to pdf. But printing to pdf might not work in all cases. For example, in Matlab, if the figure has a 3D plot and many images, it will export it as a rasterized image that is not editable in Adobe Illustrator.

4. Is there another method to import figures from matlab? sometimes my plots are just too heavy for the copy menu and when I paste them to Ai it becomes a solid image.

Yes, there are ways to force Matlab to avoid it being exported as a solid image, but they don’t always work. First, in the Edit tab of the figure menu, click “Copy Options”, if Clipboard format says “Preserve information (metafile if possible)” change it to “Metafile (may lose information).” If that doesn’t work, in the Matlab command line, type saveas(gcf,’test.pdf’). The saveas function sometimes does a better job than the clipboard. However, this even fails to work in some cases. The following user generated code https://www.mathworks.com/matlabcentral/fileexchange/23629-export_fig sometimes works where other efforts fail. If all these efforts fail then you will have to resort to screen shots.

5. Would we be able to do this with figures created in R?

See answer above.

6. If we are using python, can we also do such copy-pasting things and modify the figures?

In python you need to do the following:

import matplotlib.pyplot as plt

plt.rcParams[‘svg.fonttype’] = ‘none’

Then, either type plt.savefig(‘test.svg’) or in the figure menu click the save button and select scalable vector graphics and save the figure. Then, in Adobe Illustrator open the file. You should be able to edit the figure. I found this information in the following YouTube video Python data visualization in Adobe Illustrator.

7. How you select items without selecting the background?

Please see the video Working with backgrounds in Adobe Illustrator.

8. What is the best way to create a text box?

For a small amount of text, simply click on the Text tool and click on the screen with the left mouse button. If you want to write a paragraph click and hold down the left mouse button drag the mouse to make the size of text you like. These are not the only methods but the best.

9. Can you show how to insert a graph from Excel to edit?

Simply Ctrl+C to copy the Excel graph and then paste in a document on Illustrator. Then, go to the menu bar and click “Object”>”Clipping Mask”>”Release.” Keep releasing the clipping masks until this option is greyed out. Then, go to the menu bar again and click “Object”>”Compound Path”>”Release” until this option is greyed out. The graph is now a grouped, you need to double-click to edit the components. Or, right-click with the mouse and select “Ungroup.”

10. Can you go through inserting Matlab data again?

Simply select “Edit”>”Copy Figure” and then in Illustrator type Ctrl+V to past. Double-click on the object to edit the components.

11. So you just joined two lines together to make the axes. If I have a bar graph and want to align the bottom line of the rectangle of the bar to the x-axis, is there a shortcut for that?

Yes, however I would caution doing this with a bar graph because this will change the position of the top of the bar as well, meaning that it will no longer reflect the average of the original data. I recommend making all graphs in a graphing program with very similar aesthetics to the final product. If this is not an issue in your particular case then you can use the align to bottom tool. Please see video Aligning objects in Adobe Illustrator.

12. Can you draw a whole brain using the Illustrator?

Drawing a human brain is quite tedious and time consuming and would take too long to do in a webinar. In the future, I may add a timelapse video on the Adobe Illustrator for Scientist YouTube channel. However, to draw it accurately, I need to trace an example on the web. It’s simply too complex and amorphous to reproduce from memory. I probably won’t upload it any time soon. A mouse brain is much easier (see video below). Please see video Draw a mouse brain in Adobe Illustrator.

13. Does joining those corners for the scale bar negate using the blunt ends? It looks like it filled in that gap and made the lines longer?

I realized this for the first time during the webinar. I made the lines extra thick during the webinar to illustrate to issue. For most error bars, the error would be less than 1-2%, in many cases less than the resolution of the image itself. However, in the interest of accuracy, I show in the video below how to make it exact. Please see video How to draw scale bars in Adobe Illustrator.

14. I use ppt for posters because my institution’s templates are in ppt; is there a way to easily move a ppt template into illustrator to make a poster?

Yes, save the file as a pdf in PowerPoint. All pdf’s are compatible with Adobe Illustrator.

15. When resizing a graph with text, the text also decreases/increases. Is there a way to keep the text at a specific size while augmenting or decreasing figure size?

Yes, a quick trick is provided in the video Changing size of graphs in Adobe Illustrator.

16. How do you copy and paste from ppt to illustrator without it changing font to symbols (especially in mac)

The best way is to save the pptx as a pdf and then open the pdf in Adobe Illustrator.

17. Can you crop images in illustrator? If not, how do you delete part of a line/pasted nerve trace?

Yes, select the image in Adobe Illustrator and click on “Crop Image.” Press the “enter” key to apply the crop to the image. This feature is new to Adobe Illustrator (added Dec 2022) so the mechanics may change in the next few updates.

18. When dealing with compound figures consisting of both, for example, ephys data and confocal data. what is the best way to go about dealing with both vector and raster based objects?

Edit the raster-based image in Adobe Photoshop or Matlab and then paste it into Adobe Illustrator. Then position and scale it accordingly in Adobe Illustrator.

19. Once you've created your new figure in Illustrator, can it now be exported in it's current form?

Yes, go to File>Export and select the format you wish. I recommend Screen resolution (72 ppi) for pptx slides and 300 ppi for manuscript figures.

20. Is it not better to save figures from python (or other programming languages) as svg?

Yes, see my answer to a question above for the method.

21. When submitting for publication, is there a preference for raster or vector images?

Journals only accept raster images. Journal of Neuroscience asks for Tiff.

22. If I’m exporting something from graphpad, would you recommend saving it as pdf or jpeg and then bringing it into illustrator?

Pdf is always a reliable bet, because Adobe created the pdf format.

23. Which figure format is the best to incorporate? PNG, TIFF, or JPEG?

My personal preference is PNG, it has a very small memory footprint and I’ve never seen compression artifacts. JPEG is probably the worst. Tiff is the format recommended by most journals because it has lossless compression, but it has a very large memory footprint.

24. Can you explain what a clipping mask is and their function? Is it best to undo clipping masks and delete them?

Clipping mask are shapes that mask or make invisible regions outside that shape. They are a very handy tool in Adobe Illustrator. If you are transferring a graph from Excel that has data outside the y-axis and x-axis limits, a clipping mask is used [automatically] when you paste that graph to hide that out-of-range data. When you release the clipping mask, then those data points will appear. This is usually the case in electrophysiological recordings when you want to focus on a small region of a long recording. It is best to use the direct select tool to delete the regions that you don’t want visible because they can slow down the computer and make the file size larger than it needs to be. Of course, you want to be careful to not delete data that might affect the interpretation of the results.

25. How to import images into illustrator, so their individual features can be modified?

You can’t. That is the major limitation of Adobe Illustrator. However, you can edit the image in Photoshop and paste it into Adobe Illustrator. If you don’t embed the image (by default it doesn’t embed) then you can edit the image in Photoshop and those changes will appear in real time in Adobe Illustrator.

26. There is another way to export from Igor to Illustrator than export to PDF?

Sorry, I am not familiar with Igor. But, export to PDF is probably your best option.

27. How do you select items without selecting the background?

The best way is to create a background layer and then lock it. Please see the video Working with backgrounds in Adobe Illustrator.

28. Can figure formats like eps and svg be imported? Would you recommend them over pdf? Thank you.

Yes, they can. For Python, svg seems to work better than pdf. But pdf works well for any other applications. Eps works, but not as well. In many cases, the distortions occur by the graphing program, not Adobe Illustrator.

29. If we already created expandable text boxes in existing ai file, is there a way to convert it to the other type?

Yes, go to the top menu click “Type”>”Convert to Area Type”

30. What's the difference between grouping and clipping mask?

Grouping doesn’t change the appearance of the objects. When you select one object it selects all objects within the group. Clipping masks group the object and the applies a mask over them. Regions of objects outside of the mask are not visible.

Helpful Links:

How to draw scale bars in Adobe Illustrator:

https://youtu.be/PqL7OdldM0g

Draw a mouse brain in Adobe Illustrator:

https://youtu.be/eZvkD-Oa-dg

Aligning objects in Adobe Illustrator:

https://youtu.be/Wz_Oz90pFvc

Transfer recording data into Adobe Illustrator:

https://youtu.be/y-9xakEObJI

Changing size of graphs in Adobe Illustrator:

https://youtu.be/Li7jqMDWqas

Working with backgrounds in Adobe Illustrator: