I need help making the jython code helping me registering individual IHC images generated by a multiplex IHC methodology that generates multiple marker images from a single section.
I have more than hundred folders and each folder have 10 tif images from the same area of the tissue section. I am using this jython perfectly for individual images but can anybody help me on modifying it to loop through all the folders? The problem is target image name changes in each folder due to case ID.
from register_virtual_stack import Register_Virtual_Stack_MT # source directory source_dir = "/path/to/source/" # output directory target_dir = "/path/to/target/" # transforms directory transf_dir = "/path/to/transforms/" # reference image reference_name = "reference_image" # shrinkage option (false) use_shrinking_constraint = 0 p = Register_Virtual_Stack_MT.Param() # The "maximum image size": p.sift.maxOctaveSize = 1024 # The "inlier ratio": p.minInlierRatio = 0.05 Register_Virtual_Stack_MT.exec(source_dir, target_dir, transf_dir, reference_name, p, use_shrinking_constraint)