I am not a graphic designer at all, but a science grad student.

I need to submit figures to a journal in .eps format, they do not accept .pdf.

When I try to convert my .pdf files to .esp, different components of the figure (plots, text) have different hues of grey instead of just being black. I strongly suspect it has something to do with how I made the figures, so let me outline my steps:

  1. Made plots etc in R, exported as pdf (these figures have a transparent background, not white).
  2. Used Pixelmator to combine plots, add text and make it all look fancy.
  3. Export from Pixelmator as pdf.
  4. Open pdf in Inkscape and save as .eps.

I tried the .esp conversion with an online tool. Same issue.

When I look at the .eps and the layers in the Pixelmator file, it seems to be that the lower on the list a layer is, the greyer it looks in the .eps. So I merged everything in one layer in Pixelmator, then exported as .pdf and converted to .eps. Same issue.

I read some things about transparency issues for .esp conversion, but I can't figure out if that's an issue. When I open the .pdf in Inkscape, everything shows up as one layer and the background seems to be set to white (checked with Ctrl+Shift+D → background). Also, while the original plots from R have a transparent background, the eventual image I export from Pixelmator has a white background.

When I export my file as a .tiff or .jpeg (300 dpi) and convert to .esp everything looks fine, by the way. However, the file becomes huge (from 600 KB to 7 MB), and the journal has size limits for uploading figures.

I have limited knowledge of these file types and have exhausted googling solutions (that I understand).

Help would be so much appreciated!

EDIT/ADDITION: when I check the pdf exported from Pixelmator in Acrobat for layers, there aren't any.

  • This may be a bug in Inkscape. See, for example, ( stackoverflow.com/questions/17245685/… ). I also see transparency related bugs exporting EPS on their bug tracker ( bugs.launchpad.net/inkscape ).
    – Yorik
    Aug 22, 2017 at 19:50
  • Sometimes, the open/save/export filters can actually fix syntax issues. You might try opeing the PDF, then saving a secondary copy using Inkscape-native format, then opening that and try exporting.
    – Yorik
    Aug 22, 2017 at 19:51
  • 1
    Does Pixelmator support vector data? Do your submitted EPS files have to be vector in nature? An EPS is just a wrapper and isn't, by default, vector. I suspect opening Pixelmator files in Inkscape is just placing the raster images in Inkscape and the color variation is coming from rich or RGB blacks. You'd be better off building everything in Inkscape and saving as an EPS there.
    – Scott
    Nov 21, 2017 at 2:48
  • 1
    What program are you using to view the EPS? Have you checked with another program to rule out the possibility that it’s just a rendering issue in the viewing program and your file is fine? (I’ve found Apple’s quicklook to sometimes be unreliable on less common file types.)
    – Wildcard
    Apr 15, 2019 at 7:42

1 Answer 1


I am not an expert in this area and have just a flirtation with graphic and text. You could use Adobe Photoshop and export the graphics to Adobe Illustrator and from there you can save as an Adobe Illustrator EPS file. This sounds a little convoluted but I do not know of an app the will expedite, I am sure anyone reading has a quicker and efficient method.

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