How to measure pollution in the air of the household atmosphere? How best to protect windows and air flows?

Consult a firm that specializes in industrial hygene. Typically they will want to know what you are testing for though (mold, radon, carbon monoxide, sulfer dioxide, methane, etc).

To protect windows and air flows you'd have to seal your house tight. Be advised this may cause other pollutant levels to rise.

If you're just looking to avoid dust/spores though a good HEPA filtration system for intake would work.

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