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I'm still using InDesign for science texts because Affinity Publisher doesn't yet have endnotes and such books have hundreds of them. One of the downsides of ID is that it doesn't have an equation editor and does a poor job of importing equations from Word. I know,. Some others and I just spent two days wresting with the troubles that creates.

Only afterward did I realize that Affinity Photo should be great for creating equations, even complex, multilevel ones with specialized characters. It's easy if a bit niggling. Just create a text box for each element and insert the needed character from the Text-Glyph Browser into that box. Photo even ships with multiple STIX fonts, which should offer everything that you need. You can then resize and move that element around to get it just right. For ID, you'll need to export it as a graphic and then place it. With Affinity Publisher you can simply incorporate that equation into your document, tweaking it as necessary.

That is all the more reason to work with Publisher when you can. Now if Publisher just did endnotes, my life would be complete.

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If you are to create separate text boxes for each equation component – would it not work similarly in any software – Publisher, InDesign? A Photo does not have any edge here I think.

If I have equation in Word I usually just export the page as PDF and copy the important part from opened PDF to layout... which is admittedly bit cumbersome.

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At least on the Mac (and I would imagine on the other platform) there are specialized tools that can work better for this than trying to use the functionality within Word and copying it across.

Note also that equation support has been discussed a few times in other threads on the forum...  a few examples (not all of them):

 

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