First thing to know: After start the game and select Saved Game, you will see every level of the game and below them somewhat of a circle, as shown in the picture. It means, that the level has a Rune to be collected. When it is Blue, it means you got it already, when Grey, you didn't yet.
Second: I will refer to each level by its name and describe where each one of the Runes are and show where with a picture I took myself.
Third: There are 13 Spirit Runes and Three Achievements related to them: Collect a spirit rune, Collect Half Of The Runes and Collect All Runes.

I hope, you find this helpful. Any problens or considerations, let me know in the Comments.

T.K.

Side Note: Some of the pictures won't be showing the Rune, but I am pretty sure they are right. In any case, mistakes can be made.

This is pretty easy to find, lead Ataataq up instead of going down, right after breaking through those Ice-Things. See the picture below:

After going up in those Ice-Walls one Yeti will run after Ataataq, jumping to the other border will make it fall and die. On that second border, there will be two Ice-Walls and one more Yeti. Go Left and climb it up, hard to miss it now. See the picture below:

Ok, this is really easy. It is exactly above the first Fire-Place, you can get it by climbing the huge Ice on the Right and jumping back to the Left. Up there, it will be your Spirit Rune. See the picture below:

Even if quite simple, it took me really long to find it. After throwing the huge Ice down and breaking the Ice-Bridge go up on the Ice-Wall. Make sure to go right fruther as you can, it will be there waiting. Look the picture below:

This one is almost impossible to miss, as you will see it, if you are to progress in the game at all. See the picture below:

Well, at a point in the level, you will climb an Ice-Wall with Ataataq and something will fall on a plataform on the other side. Jump to that plataform, break the ice and you will find it. See the picture below:

I also don't think, it is possible to miss this one, as while progressing through the level you will find it. After blocking the Yeti, the second one, just move left and you will find it, as you must go down to continue. See the picture below:

Playing the level a Ataataq you will reach a Fire-place, you will have two ways: Go up or break through black-things. There you will have it. See the picture below:

Playing as Ataataq, you will have to climg an Ice-Wall right at the start, by the end of it, you can go up or face a snow-wall. If you face the snow-wall, you will be able to break it. Continue and you have it. See the picture below:

This one also, it can be easily find by simply playing the game. See the picture below, it is a well recognizable place in the second level inside the Sos:

At the start of the level, you will be chased by one of those Anubis or something, after falling the next area before an Ice-Wall and leaving it behind, the Rune is behind that Wall. See the picture below:

With both Anubis-thing behind you, you will probably run right all the time, after leaving both of them behind, you will find this Rune on the Left side. See the picture below:

This is not hard to find. At some point of this level, you will be using many Ice-Walls to go places untill you use a longer one to go up at the left side of the level. If you go up the whole way, you will find your Rune. See the picture below: