The CNN_Smoothie pipeline presented here provides a novel framework that can be easily implemented for many different applications, including immunohistochemistry grading and detecting tumor subtypes and biomarkers. We revised the available Slim codes to fit the algorithms for running them on CPUs. For  additional information and reference, please check the pre-print describing the method here:

Deep Convolutional Neural Networks Enable Discrimination of Heterogeneous Digital Pathology Images

Pegah Khosravi, Ehsan Kazemi, Marcin Imielinski, Olivier Elemento, Iman Hajirasouliha
EBioMedicine (December 2017)

The link to the published journal version: http://dx.doi.org/10.1016/j.ebiom.2017.12.026

The Readme file is divided into two parts:

1) for running the CNN_basic algorithm look at the Readme at CNN_basic file.

2) for running other architectures of CNN such as Inception and ResNet look at the Readme in the "scripts" directory.