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I'm making species distribution maps and have got the Atlas working perfectly using a polygon layer to show the quarter degree grid cells for species observation records. I have ~ 250 species.

The problem is that I have for most species a predicted ecological niche model (raster) which I would also like to display on the map and I can't find a way to do this using the Atlas functionality.

There's a very helpful post showing how to use rule based symbology for another polygon file but not for rasters (Filtering features in other layers of QGIS Atlas)

Does anyone know how to solve this problem?

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Came across a similar problem, a possible and simple workaround is to convert your raster into a vector using "Raster pixels to polygon" which is a QGIS native algorithm.

Then, use a join operation to link your coverage layer with the created vector layer in the previous step.

Then, use the same rule-based styling as suggested on the link that you provided.

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