The ground glass infilitrates were caused by alveolarseptal amyloidosis. The CT showed a uniformity of ground glass infiltrates, without a mosaic pattern. The pathology images above include H&E, congo red and crystal violet stains which are typically used to confirm the diagnosis. The fibrils were also birefringent but this could not be photographed. These were samples obtained by transbronchial biopsy.
This case was used as a clinical vignette for the 2nd year medical students. Above is the paper written by Nicholas Braus (click on the clinical-practice-essay icon) which is an excellent review of the pathophysiology of this disorder. I invite you to read it.