bioimage_analysis

Evaluation of biological effects from microscopy images

Official GitHub repository of our study "On the objectivity, reliability, and validity of deep learning enabled bioimage analyses". You can find a preprint of our paper on Biorxiv, and all source data, our open-source model library, two entire bioimage datasets, as well as the source code in our Dryad repository.

Here, we provide all source code that can be used to reproduce our analyses and a Jupyter Notebook, optimized for the use in Google Colab, to train deep learning models according to the strategies we investigate in our study. Furthermore, we also share all of our training datasets with the open science community.

Local installation

To reproduce our experiments a Python (>= 3.6) installation is required. Run the following code to set up the environment

git clone https://github.com/matjesg/bioimage_analysis.git
cd bioimage_analysis
pip install requirements.txt

The code requires a TensorFlow 1 installation (tested on TensorFlow 1.14.0 and 1.15.2). For more information see the TensorFlow install guide.