MATLAB functions for image analysis of branched organ structures (such as the pancreas). See details: STAR Protocols
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Download test data folders
raw_images_tif_files
andoutlines_mat_files
from Mendeley Data. (574MB) -
Make sure that current Matlab directory contains the folders
raw_images_tif_files
andoutlines_mat_files
and all function .m files listed further below: -
Run
'demoScript_OneImage_ManualInput.m'
to see an example of a script that analyses one image with manual input from the user during the run. -
Run
'demoScript_Batch_NoInput.m'
to see an example of a script that analyses all 7 sample images with no manual input from the user. -
Note that both scripts require 'Image Processing Toolbox' and 'Statistics and Machine Learning Toolbox' and 2018a version MATLAB or newer to run.
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Functions called by
demoScript_OneImage_ManualInput.m
anddemoScript_Batch_NoInput.m
:
segmentDAPIimage.m
tipScoreIm.m
returnTableWithCellInt.m
returnTableWithCellPairInt.m
S. Heilmann, H. Semb, P. Nyeng. Quantifying spatial position in a branched structure in immunostained mouse tissue sections. STAR Protocols, 2021.