We collaborate closely with web platform developer groups in medical image computing (OHIF, dcm.js, Kheops, etc.), so we are well aware of the current status, challenges, and trends. Web platforms started from scratch and in a few years they can now do basic (2D-oriented) image viewing and annotations, volume rendering (the feature set equivalent to desktop platforms of about 10-15 years ago). There is now a rethinking/retooling in progress to break into true 3D processing (e.g., moving to 3D libraries, such as itk.js, vtk.js). With this, there is a convergence of web and desktop platforms, especially at lower level libraries. We’ll probably end up having all basic features (3D oriented image viewing, annotation, and processing) in web platforms in a couple of years and desktop/server will remain for high-end, specialty applications, and large/complex data processing.
Since your problem is already solved on desktop/server-side, one option is to leverage that (e.g., using 3D Slicer features via web services). This is the approach taken by several web applications today.
Another option is to wait a few years for web platforms to mature and have stronger 3D support (adopt vtk.js, have segment editing infrastructure, etc.). You can speed this up by contributing to these web platforms and pushing development of specific features that you need (e.g., segmentation data management).
A third option is to develop solutions that only work for your project and not aim for general usability, stability, sustainability, etc. Although this is not a long-term solution and does not move the field of medical image computing forward, you may fulfill your project’s needs much faster than developing/waiting for general solutions, so it may be a valid business strategy, too.