What is CDeep3M Our goal with CDeep3M is to make deep learning algorithms available to the community and improve reproducibility. We built CDeep3M as a containerized tool, using deep learning for large-scale image segmentation tasks. It is an open source development and the software is free to use. You can run CDeep3M on your local platforms, on cloud providers, on GPU clusters or with free GPU resources on this website (limitations to the amount of data being processed on this website apply). Pre-trained models for electron and light microscopy (EM and LM) data are available here.