Accurate colony counting is crucial for assessing microbial growth in high-throughput workflows. However, existing automated counting solutions struggle with the issue of merged colonies, a common occurrence in high-throughput plating. To overcome this limitation, we propose MCount, the only known solution that incorporates both contour information and regional algorithms for colony counting. By optimizing the pairing of contours with regional candidate circles, MCount can accurately infer the number of merged colonies. We evaluate MCount on a precisely labeled Escherichia coli dataset of 960 images (15,847 segments) and achieve an average error rate of 3.99%, significantly outperforming existing published solutions such as NICE (16.54%), AutoCellSeg (33.54%), and OpenCFU (50.31%). MCount is user friendly as it only requires two hyperparameters. To further facilitate deployment in scenarios with limited labeled data, we propose statistical methods for selecting the hyperparameters using few labeled or even unlabeled datapoints, all of which guarantee consistently low error rates. MCount presents a promising solution for accurate and efficient colony counting in application workflows requiring high throughput, particularly in cases with merged colonies.