#Confocal images analysis for study of Eli Lilly Images

##Packages to install

###opencv:

Clone the opencv repo at https://github.com/Itseez/opencv. Follow the instructions for installation on Linux at http://opencv.org/. Add to ~/.bashrc :

export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/usr/local/lib

To test sample opencv code, compile using

g++ < file_name > `pkg-config opencv --cflags --libs`

##Build and run image analysis package

• Inside the project root directory, type make to build the project. A binary called analyze will be created.

• Command to run the software:

./analyze < image directory path with / at end >

• Image directory path should have a original directory which contains the separate tiff images for the RGB layers.

• image_list.dat has to be created inside the image directory path. This tracks the different images that are being processed and allows selective processing of one or more images.

##Result

• Inside the image directory path, a directory called result gets created. This contains the raw, enhanced and analyzed images for each image.

• The computed_metrics.csv contains the metrics results generated during the analysis.