cif-reader

This module reads images from imaging flow cytometry data files (.cif files) into a tensor in python.

Requirements

python 2.7

pip

bioformats

$ pip install bioformats

javabridge

$ pip install javabridge

numpy

$ pip install numpy

math

$ pip install math

Use

Imaging flow cytometry (IFC) instruments by Millipore generate compensated image files (.cif files), which contain images and metadata. This module reads images from cif files into a tensor in python. Optionally the images are padded and cropped such that they have the same dimensions. The image data in the tensor can then readily be fed, e.g., into deep learning networks such as convolutional neural netowrks.

read images from cif files into tensor T:

$ import ifc

$ filelist = ['blasts.cif', 'normal.cif']

$ T = ifc.read_cif(filelist)