Induced sputum, bronchoalveolar lavage (BAL) or biopsy specimens may be submitted to the laboratory for investigation. Smear, touch or imprint preparations are most often used when little biopsy material is obtained from transbronchial biopsy, paraffin or frozen sections when larger amounts of lung tissue are available, for example after post mortem examination. The prepared specimens are examined microscopically with a cytochemical method such as Toluidine blue O staining or an immunological procedure such as immunofluorescence.

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