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As per the title I compared my system against two other systems separately but I'm worried about it coming across as that it was a three way comparison.

Neither of the below titles convey what I want to, what is the best way to word a comparison such as this or would it be better being split into two chapters?

Comparison of egocentric camera vs. static camera vs. dense sensor placement.

Comparison of egocentric camera against static camera and dense sensor placement.
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The clarifier you want is "respectively." It's fine in running copy, or even as a caption, but clunks as a header.

Comparison of egocentric camera against static camera and dense sensor placement, respectively

For a headline, you might try emphasizing the idea that there are two comparisons with some redundancy:

Comparisons of Egocentric Camera vs. Static Camera and vs. Dense Sensor Placement

0

"Here, we see that the egocentric camera is being compared with either the static camera or the dense sensor placement." You can also add "Please note that this is not a comparison between the static camera and dense sensor placement. Such a comparison is inappropriate because ..."

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    As simply a title, I would write: "Egocentric Camera and How It Compares to either Static Camera or Dense Sensor Placement" – Stu W Nov 5 '15 at 18:07

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