Image library for internal usage of Nanobiotechnology team

There are preliminary packages for imlib.

pip3 install tifffile
pip3 install tqdm
pip3 install numpy
pip3 install scipy
pip3 install pandas
pip3 install pims

brew install opencv4

pip install "https://github.ibm.com/kimsung/imlib.git"

opencv is a package hard to install. In macOS, use homebrew and in Ubuntu, use apt-get to install opencv. (Currently - 20190325, opencv4 is a mainstream version.)

For best practice, I recommend to use jupyter notebook. In IBM network, you can log in nanobio.watson.ibm.com and start jupyter notebook session.

To analysis tiff images in a single directory, move to the directory of interest.

import imlib

imgfolder = imlib.ImgFolder('.')
imgfolder.preview()

These commands create ImgFolder object and it automatically include all images inside a current directory. preview() method creates thumbnail images of all files.

tif = imgfolder.get(1)
tif.mean()

You can analyze an individual file by using get() method and it returns ImgBase object which has basic functions for analysis. mean() method gives the averaged image over all frames.