MUSCIMarker is an open-source tool for annotating visual objects and their relationships in binary images. It is implemented in Python, known to run on Windows, Linux and OS X, and supports working offline. MUSCIMarker is being used for creating a dataset of musical notation symbols, but can support any object set.

The user documentation online is currently (12.2016) incomplete, as it is continually changing to reflect annotators' comments and incorporate new features. This version of the software is not the final one, and it is under continuous development (we're currently working on adding grayscale image support with auto-binarization, and Android support for touch-based annotation). However, the current version (1.1) has already been used to annotate more than 100 pages of sheet music, over all the major desktop OSes, and I believe it is already in a state where it can be useful beyond my immediate music notation data gathering use case.