Small- and medium-sized manufacturers need innovative data tools but, because of competition and privacy concerns, often do not want to share their proprietary data with researchers who might be interested in helping. This paper introduces a privacy-preserving platform by which manufacturers may safely share their data with researchers through secure methods, so that those researchers then create innovative tools to solve the manufacturers' real-world problems, and then provide tools that execute solutions back onto the platform for others to use with privacy and confidentiality guarantees. We illustrate this problem through a particular use case which addresses an important problem in the large-scale manufacturing of food crystals, which is that quality control relies on image analysis tools. Previous to our research, food crystals in the images were manually counted, which required substantial and time-consuming human efforts, but we have developed and deployed a crystal analysis tool which makes this process both more rapid and accurate. The tool enables automatic characterization of the crystal size distribution and numbers from microscope images while the natural imperfections from the sample preparation are automatically removed; a machine learning model to count high resolution translucent crystals and agglomeration of crystals was also developed to aid in these efforts. The resulting algorithm was then packaged for real-world use on the factory floor via a web-based app secured through the originating privacy-preserving platform, allowing manufacturers to use it while keeping their proprietary data secure. After demonstrating this full process, future directions are also explored.