This repository contains the code for https://www.sciencedirect.com/science/article/pii/S0092867420301112.
In this repository you will find the ressources to perform all deep learning and image analysis tasks described in the article "Cellular and Molecular Probing of Intact Human Organs", including training a convolutional neural network, predicting a binary mask on tissue-cleared images and counting cells on binary masks.
Python 3.6 Numpy Scipy PyTorch 1.2 Nibabel https://github.com/seung-lab/connected-components-3d