[3] Congo blue, however, is in widespread international use, in gel sheet form, as a filter to place in front of theatrical, motion picture, television, church, and live event lighting instruments.

The Congo Blue filter effectively removes the color from chart and shows the separate bars only in terms of their differing incremental brightness levels.

The proposed mechanisms suggest hydrophobic interactions between the aromatic rings of the dye molecules, leading to a π–π stacking phenomenon.

In histology and microscopy, Congo red is used for staining in amyloidosis, and for the cell walls of plants and fungi, and for the outer membrane of Gram-negative bacteria.

Apple-green birefringence of Congo red stained preparations under polarized light is indicative of the presence of amyloid fibrils.

Additionally, Congo red is used for the diagnostics of the Shigella flexneri serotype 2a, where the dye binds the bacterium's unique lipopolysaccharide structure.

Furthermore, Congo red may also be used to induce expression of the type III secretion system of Shigella flexneri, bringing about the secretion of IpaB and IpaC, which form translocation pores within host cell membrane, allowing effector proteins to pass through and alter the host cell's biochemistry.