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Spheroids and organoids can be imaged while they are still embedded in Matrigel matrix depending on the magnification and what is being imaged. In fact this may be necessary for live/dead staining and organoid swelling assays. We have found that the sandwich/overlay workflow method, wherein cells are seeded on top of a thick layer of Matrigel matrix are easier and faster for imaging as the spheroids are mostly on a single focal plane. Alternatively, small Matrigel matrix droplets are also thin enough for fast imaging at low magnification. For marker staining of larger organoids at higher magnifications or when organoids are embedded in a thick gel it might be helpful to remove structures prior to staining. If you do need to remove cells from Matrigel matrix, we recommend Corning cell recovery solution for cells/spheroids cultured in Matrigel matrix. This solution will allow non-enzymatic retrieval of spheroids and organoids. It can de-polymerize a thick Matrigel matrix layer at 4°C and facilitate cell retrieval. Here is a protocol. It should also be noted that certain fixatives such as paraformaldehyde can depolymerize Matrigel matrix. If it is desired for the Matrigel matrix to remain intact adding up to 1% glutaraldehyde to fixative can help.