Matlab scripts and Fiji macro for analyzing images of cleared cochlea immunostained with anti-MYO7A antibody using 3D watershed method.
This program needs:
- Matlab (R2017b or newer version)
- Fiji (https://fiji.sc/)
- "CLASSIC WATERSHED" plugin for Fiji (https://imagej.net/Classic_Watershed)
- Please install this plugin in advance.
Data size: Total 48 MB - Program 6 KB - Test data 48 MB
For testing the program, please run the scripts/macro as follows:
- Run "Watershed_main1.m" on Matlab, which calculates threshold value.
- Open "Watershed_main2 (macro for Fiji).txt".
- Make sure that "threshold" value in line 2 is the same as the value calculated in step 1.
- Close "Watershed_main2 (macro for Fiji).txt".
- Start Fiji and open "linearizedIm2.tif".
- Run "Watershed_main2 (macro for Fiji).txt" on Fiji.
- Save resulting "watershed.tif" file.
- Run "Watershed_main3.m" on Matlab.
It takes ~5 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 "..\Results":
- "innerImage.tif", "outerImage.tif" (Images indicating detected cells)
- "detectedHairCells.xlsx" (Coordinates of detected cells; sheet1:IHCs, sheet2:OHCs)
October 30, 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]