Instructions for Downloading CurveAlign
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Standalone for Windows:
1. Download and install Matlab MCR 7.17 2012a for Windows 64-bit.
2. Download and run CurveAlign_V3.0_Beta2_WIN64
Standalone for MAC:
1. Ensure you have the required Java SE version 6 for x86_64 (not included in OSX 10.9 - Mavericks - and above):
From the Mac terminal, run:
If you do have it, note the directory where Java SE 6 is located. e.g. /Library/Java/JavaVirtualMachines/jdk1.6.0.jdk/Contents/Home
If you don't have it, install it from http://support.apple.com/kb/DL1572 then run the above command again to find the Java 6 SE directory.
2. Download and install the MATLAB Compiler Runtime (MCR) MCR 7.17 2012a for Mac.
NOTE: If you did not have Java SE 6 installed by default in step 1 you will need to manually install the MCR:
In your terminal, navigate to the MCR_R2012a_maci64_installer directory and execute the command:
./install -javadir /Library/Java/JavaVirtualMachines/jdk1.6.0.jdk/Contents/Home
(with the Java 6 path updated appropriately based on the path you found in step 1)
3. Launch the APP: right click the APP(ctrl -click)----->Show Package Contents ----> Contents---->MacOS---->applauncher (right-click and choose open).
4. Depending on the OS version, X11 might need to be installed to successfully running the APP. Just follow the instructions from the pop-up window to complete the installation.
Download and unzip the Matlab m-files above. Then go to curvelet.org and register to sign a licensing agreement and download the CurveLab 2.1.2 MATLAB package. Place the folder "CurveLab-2.1.2" into the CurveAlign folder("MatlabCode_CA3.0_Beta_LOCI"). With MATLAB's Current Folder set to the CurveAlign folder, enter "CurveAlign" at the command prompt to launch the GUI.
Installation and Usage
- Output data and images are saved under a subfolder named \CA_Out\ within the folder where the original image exists, and under filenames indicating the source of the data and the type of output.
- To read in the output files from CT-FIRE, CT-FIRE output .mat files should be saved in the same folder as the original images.
- To read in the boundary files (in .csv or .tif format), the boundary files should be saved in the same folder as the original images and should follow the strict naming convention, e.g., if image is named: "1B-a5.tif", CSV boundary is named "Boundary for 1B-a5.tif.csv", and tiff boundary is named " mask for 1B-a5.tif.tif "
- Tiff boundary files must be 8bit binary mask images where the inside of a region has a value of 255 and everything else must be 0. Boundary tiff files must have the same number of pixels (length and width) as the original image and may be produced by hand or by segmentation in ImageJ/FIJI.
- Tiff boundary is recommended for more accurately extracting the features of collagen-cell interaction.
-To run feature ranking, an annotation .xlsx file should be prepared and saved in the same folder as the .mat feature files. This file is named as "annotation.xlsx" with two columns, where the first column includes the label for each image( e.g.: 1 for positive, 0: negative ), the second column includes the full original image name.
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