The invention features particle removal assemblies and methods for removing dust and other debris from a sample container, e.g., to improve counting colonies of microorganisms (e.g., bacteria, fungi, or protists) present in environmental, pharmaceutical, biological, and other samples. An assembly of the invention includes components for particle removal, e.g., a filter, a dryer, a flow controller, and an outlet. The invention also provides methods of detecting samples after cleaning a sample container with clean and / or dry gas.