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Wikipedia has an extensive set of anatomy SVGs, but I can't highlight different organs or parts dynamically, because there are no source files with layers I can manipulate in Photoshop or GIMP.

How can I edit an .SVG file?

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An .SVG file IS a source file. It isn't layers in the Photoshop/Gimp sense but it absolutely can be picked apart. Use an SVG editor - that would be Illustrator or Inkscape.

Alternatively, if you want to get real crazy you can open the .SVG in any text editor and look for the values you want to change which for colors would be in Hex format #nnnnnn

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    Worth emphasising the key difference - in general, SVG, Illustrator and Inkscape work with vectors, Photoshop and Gimp work with raster images – e100 Mar 22 '12 at 9:46
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    Also worth noting that Inkscape is free, cross-platform and open source. – Matt Bracewell May 14 '15 at 11:15
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You can try SVG-edit, BlueGriffon, GLIPS Graffiti, Free SVG Editor and many other software listed in this URL: http://listoffreeware.com/list-of-best-free-svg-viewer-software-for-windows/ for viewing and editing SVG files.

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    Which software do you use, what is the advantage of it and what the disadvantage? – Mensch Dec 30 '14 at 13:15
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This tool might help you to edit the svg file.

SVG Editor

We're looking for long answers that provide some explanation and context. Don't just give a one-line answer; explain why your answer is right, ideally with citations. Answers that don't include explanations may be removed.

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    There are lots of SVG editors. Is this one any good? – usr2564301 May 9 '15 at 9:14
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    Can you please elaborate on your answer? As it stands, it is a link-only answer that becomes useless if the link rots and may be deleted for that very reason. – Wrzlprmft May 9 '15 at 9:30

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