You have published this really cool Segmenter for subcellular structure segmentations. I also saw that you have been using images of single cells, e.g. in the integrated cell models and in the Cell Viewer. I assume those were segmented single cells? What method are you using to segment cells in 3D? The Segmenter tool seems optimized for subcellular segmentation, not cell segmentation.
Also, I’ve seen that you have worked with CellProfiler and committed code to CP for 3D support. Would you be willing to share an example segmentation pipeline that you use for 3D segmentation in CellProfiler, if you have something like this?