Given an input IMOD model file, MRC file, and a stack of segmentation images with the same dimensions as the MRC file, segmask will produce an output IMOD model file consisting of all segmented objects contained within the boundary of the input IMOD model file. This is most often used to create a model file consisting of all segmented organelles contained within a manually segmented cell boundary.
Scripts are also provided to run segmask on a cluster with SGE. In this way, numerous masks can be generated in parallel by submission of an array job.
To run using a single IMOD mask model file:
segmask/segmask.py input.mrc input_mask.mod /path/to/segmentation/stack
To submit a SGE array job with numerous masks on a cluster:
segmask/grid/run_segmask.sh input.mrc /path/to/mask/files /path/to/segmentation/stack
Both segmask.py and run_segmask.sh support a number of the same arguments. These arguments control a variety of important parameters during the masking process, as well as enable postprocessing steps to mesh, filter, and sort each output model file. To view the complete list of arguments, view segmask's help:
segmask/segmask.py -h