Code overview

The tumor lightsheet image analysis code is organized into 5 modules that include data pre-processing, segmentation, segmentation post-processing, distance transformation, and penetration profile generation. (See the pipeline overview HERE)

This code can be operated as either:

• An automated pipeline: which can analyze a dataset with minimal user input, or

• A manual pipeline: which allows each module in the pipeline to be run separately, allowing further user defined customization.

See the sections on code modules HERE and code usage for more details HERE.