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A 59 year-old woman with chronic renal disease presented in renal failure with a creatinine of 4.1 mg %. She had had a Roux-en-Y gastric bypass performed 10 years earlier. A diagnosis of oxalate nephropathy was made on renal biopsy. Oxalate nephropathy is a known complication of gastric bypass. Calcium and oxalate in the intestine form calcium oxalate complexes that are then excreted. In the setting of fat malabsorption/enteric hyperoxaluria, enteric free fatty acids are elevated and bind calcium within the intestinal lumen, inhibiting the formation of calcium oxalate. The increased amount of soluble free oxalate is absorbed by the colonic mucosa, and this is enhanced by free fatty acids and bile salts. The absorbed oxalate is excreted by the kidney and then deposited in the renal parenchyma forming stones. The renal biopsy from this patient was serially sectioned at ~ 2 microns. The oxalate deposited in a small area was then characterized in three dimensions using custom software (https://slide-atlas.org) to align serial sections of whole slide images. The segmented oxalate crystals were then rendered into a three-dimensional construct. Supplementary Material Movie Figure 1 Renal biopsy, H&E stain. Oxalate crystals segmented prior to volume rendering (one of ~ 70 serial sections shown). Scale bar 50 um.

A 59 year-old woman with chronic renal disease presented in renal failure with a creatinine of 4.1 mg %. She had had a Roux-en-Y gastric bypass performed 10 years earlier. A diagnosis of oxalate nephropathy was made on renal biopsy. Oxalate nephropathy is a known complication of gastric bypass. Calcium and oxalate in the intestine form calcium oxalate complexes that are then excreted. In the setting of fat malabsorption/enteric hyperoxaluria, enteric free fatty acids are elevated and bind calcium within the intestinal lumen, inhibiting the formation of calcium oxalate. The increased amount of soluble free oxalate is absorbed by the colonic mucosa, and this is enhanced by free fatty acids and bile salts. The absorbed oxalate is excreted by the kidney and then deposited in the renal parenchyma forming stones. The renal biopsy from this patient was serially sectioned at ~ 2 microns. The oxalate deposited in a small area was then characterized in three dimensions using custom software (https://slide-atlas.org) to align serial sections of whole slide images. The segmented oxalate crystals were then rendered into a three-dimensional construct. Supplementary Material Movie Figure 1 Renal biopsy, H&E stain. Oxalate crystals segmented prior to volume rendering (one of ~ 70 serial sections shown). Scale bar 50 um. Figure 2 Three-dimensional construct of renal oxalate crystals created from the same region seen in Figure 1 using ~ 70 serial sections and representing a total tissue volume of ~ 2.7 mm3. The crystals occupy ~ 6.8 % of the tissue volume (The 3D structure of the crystals is best appreciated in a movie included as supplementary material).