Automated needle segmentation

[fedorov]

It may be helpful to automatically segment the needle (or segment with minimum user interaction by clicking at the entry point or at the needle tip) to provide quick feedback to the user about the distance to the target, deflection, etc. To achieve this:

1. Code should be structured in such a way that needle segmentation is abstracted to support integration of different needle segmentation tools.

2. We can start with the existing needle segmentation functionality from NeedleFinder to support automated segmentation. See details and discussion here: https://gist.github.com/gpernelle/c5b1618d170f08bd92713270026d6263. As the fist step, the NeedleFinder code should be refactored to make it easier to use the segmentation functionality from SliceTracker. In the future, the may be automatic segmentation tools based on deep learning.

[che85]

Once the automatic needle segmentation is available from @mehrtash:

• [ ] Integrate into SliceTracker
• [ ] Execute for every needle image
• [ ] Think about how to store the information in metadata
• [ ] Save needle-tip and label:
  • filenames:
  • "{SeriesNumber}-needle-tip.fcsv"
  • "{SeriesNumber}-needle-segmentation.nrrd"
• [ ] rotate volume to plane of needle trajectory
• [ ] add option to rate needle segmentation result
• [ ] add option to disable needle segmentation to settings

[mehrtash]

@fedorov @che85 prostate needle finder is added to the DeepInfer model repository.

[fedorov]

@mehrtash great, thanks!

Considering other deadlines, our main priority in the time left this month is to integrate preop prostate segmentation into the workflow, and then consider needle segmentation.

[mehrtash]

@fedorov That is already integrated into the deepinfer prostate-segmenter model.

[fedorov]

@mehrtash I understand, I was referring to the items we need to do on the SliceTracker side to take advantage of the DeepInfer tools. Now that the prostate segmentation model is available, we need to integrate it into the workflow, and for the needle segmentation integration we discussed adding items listed here https://github.com/SlicerProstate/SliceTracker/issues/254#issuecomment-318468313, which is not completely trivial.