Move instance segmentation module to `run_patch` CLI

[smguo]

Issue

Currently semantic segmentation and instance segmentation share the run_segmentation.py CLI. However, Dynamorph uses non-DL approach for instance segmentation which has quite different parameter set from the DL-based semantic segmentation module. This causes confusion on which parameters belong to semantic segmentation or instance segmentation modules. For examples, multiprocessing of instance segmentation is controlled by gpu_ids parameter, even though the module runs on CPUs.

Solution

Move instance segmentation module to run_patch CLI. This will also allow possibly run instance_segmentation and then extrac_patches steps in a single command.

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