/TipScore

MATLAB functions for image analysis of branched organ structures (such as the pancreas).

Primary LanguageMATLABGNU General Public License v3.0GPL-3.0

TipScore

MATLAB functions for image analysis of branched organ structures (such as the pancreas). See details: STAR Protocols

  • Download test data folders raw_images_tif_files and outlines_mat_files from Mendeley Data. (574MB)

  • Make sure that current Matlab directory contains the folders raw_images_tif_files and outlines_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.

  • Functions called by demoScript_OneImage_ManualInput.m and demoScript_Batch_NoInput.m :

segmentDAPIimage.m
tipScoreIm.m
returnTableWithCellInt.m
returnTableWithCellPairInt.m

Graphical abstract:

Screen Shot 2021-07-07 at 13 04 12

S. Heilmann, H. Semb, P. Nyeng. Quantifying spatial position in a branched structure in immunostained mouse tissue sections. STAR Protocols, 2021.