Matlab scripts for analyzing images of cleared cochlea immunostained with anti-MYO7A antibody (hair cell marker).
This program needs:
- Matlab (R2017b or newer version)
- Image Processing Toolbox
- Statistics and Machine Learning Toolbox
- Neural Network Toolbox
Data size: Total 539 MB - Program 77 MB - Test data 462 MB
For testing the program, please run the following scripts from top to bottom:
- main0.m (unzip test data, 1 min.)
- main1.m (make linearized image, 15 min.)
- main2.m (detect inner hair cells, 5 min.)
- main3.m (detect outer hair cells, 3 min.).
- main4.m (analyze spatial distribution of outer hair cells, <1 min.)
- main5.m (make cellular cartography, <1 min.)
- main6.m (simulation of clustered cell loss, 10 min.)
It takes ~30 minutes for running all the scripts on PC with: Windows 10 Home, Inter Core i7-6700 CPU @ 3.40GHz, 16.0GB RAM.
Following result files will be saved in "..\TestData\Result":
- "linearizedIm1.tif", "linearizedIm2.tif" (Linearized images of organ of Corti)
- "innerHairCells.tif", "outerHairCells.tif" (Images indicating detected cells)
- "innerHairCells.xlsx", "outerHairCells.xlsx" (Coordinates of detected cells)
- "standardized_OuterHairCells.tif" (Standardized image of cellular distribution)
June 22, 2018
Tadatsune Iida Department of Cellular Neurobiology, Graduate School of Medicine, University of Tokyo Email: tadiida@m.u-tokyo.ac.jp
Shigeo Okabe Department of Cellular Neurobiology, Graduate School of Medicine, University of Tokyo Email: okabe@m.u-tokyo.ac.jp