A module and scripts for analysis of whole-mount in-situ hybridisation images.
The package consists of isimage module and analyse_image and select_images command line scripts. Test data and images for the scripts will be installed in the corresponding subfolders of isimage package.
The package depends on OpenCV >= 3.0.0. Please install it from www.opencv.org. Multithreading functionality of select_images script depends on IPython.parallel, however this dependency is optional.
Windows: The easiest way, is to install Anaconda package first. Then run pip and command line tools in Anaconda’s console.
Linux: Before installation please make sure you have jpeg-dev and tiff-dev packages installed.
Then run pip install isimage
Command line tools usage examples:
analyse_image -i <isimage installation path>/isimage/analyse_image/test_images/17-BLIMP-DOR003.jpg -o test_result.pptx
select_images -g <isimage installation path>/isimage/select_images/test_tasks.txt -c <isimage installation path>/isimage/select_images/cleared_model.dump -r result -p8