Background: Calmodulin-dependent protein kinase II (CaMKII) is upregulated in diabetes mellitus (DM), leading to the overproduction of collagen in the myocardium. We hypothesized that CaMKII also stimulates the extracellular matrix production in the kidneys leading to mesangial matrix expansion, a hallmark of diabetic nephropathy and a major cause of renal failure. To test this hypothesis, we developed an automated process of mesangial matrix measurement. Methods: We induced Type 1 diabetes (DM1) in wild type female FVB mice via an intraperitoneal injection of Streptozotocin (STZ, 200 mg/kg ip) and studied the dynamics of mesangial matrix fractional area (MMFA) over 10 weeks (W) in mice with: DM , DM/KN93 , 6 W after STZ, followed by 4 W treatment with a CaMKII inhibitor KN93 (70 μg/kg/day, via mini pump), and Control (C) (vehicle only) mice. Both kidneys were retrieved. MMFA measurements were performed on 50 glomeruli from each animal on trichrome-stained paraffin sections using a trainable segmentation WEKA (Waikato Environment of Knowledge Analysis) plugin for Fiji, as well as on the electron micrographs of 4-5 whole glomeruli/animal. Results: Both DM and DM/KN93 mice were severely hyperglycemic (517 and 538 mg/dL compared to 161 mg/dL in C). In DM mice, the kidney weight increased by 76% and the MMFA significantly increased by 81% compared to C (9.4 ± 1% vs 5.2 ± 2.8%). In DM/KN93 mice, MMFA was similar to that in controls (6.2 ± 2.3%). The electron microscopy study has confirmed these MMFA changes. Other features of human diabetic nephropathy were not seen and the fractional mesangial cell area and the fractional podocyte area were relatively unchanged in DM and DM/KN93 mice. Conclusions: Our DM1 mouse model reproduces the key features of early human diabetic nephropathy. KN93 prevents DM-induced extracellular matrix production and kidney mesangial matrix expansion, suggesting that chronic inhibition of CaMKII could be a potential treatment for the early diabetic nephropathy. Reliable automated measurement of the MM area can be achieved after training by the WEKA plugin.