okabe-lab/cochlea-analyzer

Matlab scripts for analyzing images from cleared cochlea

Matlab scripts for analyzing images of cleared cochlea immunostained with anti-MYO7A antibody (hair cell marker).

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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

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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)

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June 22, 2018

Tadatsune Iida Department of Cellular Neurobiology, Graduate School of Medicine, University of Tokyo Email: [email protected]

Shigeo Okabe Department of Cellular Neurobiology, Graduate School of Medicine, University of Tokyo Email: [email protected]