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Updated: May 25, 2026

Three-dimensional Quantification of Intestinal Mucus Using Whole-mount Tissue Imaging
Published on: September 12, 2025
Assessment of mucus thickness and production in situ
1Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden. lena.holm@mcb.uu.se
Abstract:
The nature of the mucus gel layer covering the gastrointestinal tract makes it difficult to study outside its natural site attached to the mucosa. Here, we describe a technique for intravital microscopy studies of the mucus gel layer from the stomach down to the colon in anesthetized rats and mice. Mucus thickness and accumulation rate in each segment of the gastrointestinal tract is measured with a micropipette technique under observation through a stereomicroscope. In this way, the nature of the mucus gel in vivo is readily studied, and effects of interventions or disease on the mucus can be determined in longitudinal studies or by comparing animals. Using this technique, we have been able to demonstrate that there are two forms of mucus gel adherent to the stomach and colon mucosa: one layer which is removable by suction and an underlying firm adherent gel layer, while in the small intestine, all mucus adhering to the mucosa can easily be removed.

