I'm an undergraduate working on a project where I have intestines that were fixed in formalin before I arrived. They have remained in 10% neutral buffered formalin this whole time. I am embedding in paraffin and cutting at 5 micrometers. Many of the samples vary in color and fragility from one to another. Some are white, some are dark brown, some are a translucent pink. I'm also noticing some strange issues in my stained slides. Examples: no villi present, just a solid mass of something stained slightly blue with dark blue clusters of material on the slide; what look like goblet cells all clustered in a semicircle at the end of where villi should be; obvious gaps between muscle cells in the muscularis externa. I don't think it's my staining procedure as it worked beautifully on another sample of the exact same species and tissue type. I'm starting to wonder if some of the samples were not stored correctly or quickly enough.