DeepLearningToolkit

The DeepLearningToolkit (DLTK) is a set of environments populated with several libraries related to deep learning and allows running protocols on Scipion which require deep learning tools. All of them are available for GPU or CPU only (the installator'll detect your configuraction)

Requirements

A nvidia drivers 450 or higher is required, to review the nvidia driver version please run nvidia-smi. If older version is detected, the DLTK will be installed without GPU support.

How to install

Run scipion3 installb deepLearningToolkit

It could take more than 30 minutes. To speedup the installation we propose to use libmamba solver (we experienced a x4 speedup) . It is only available for conda >=4.12 and has to be installed and setup on your conda installation. For more details, please visit: https://www.anaconda.com/blog/a-faster-conda-for-a-growing-community

List environments

• xmipp_DLTK_v0.3

• Protocols ussing it: screen_deeplearning, deep_denoising, resolution_deepres, screen_deepConsensus
• python=3.7
• scikit-image=0.14
• tensorflow=1.15
• keras=2.2
• scikit-learn=0.22
• pip
• numpy==1.21
• h5py==2.10.0

• xmipp_DLTK_v1.0

• Protocols ussing it: deep_misalingment_detection
• python=3.8
• tensorflow=2.7
• keras=2.7
• pip
• numpy==1.23

• xmipp_MicCleaner

• Protocols ussing it: deepMicrographScreen
• python=3.6
• micrograph-cleaner-em=0.35

• xmipp_deepEMhancer

• Protocols ussing it: protocol_deepEMhancer
• python=3.6
• deepemhancer=0.12
• numba=0.45

• xmipp_pyTorch

• Protocols ussing it: deepHand
• python=3.8
• numpy=1.23
• mrcfile=1.4.3
• kornia=0.6.12
• starfile=0.4.12
• pytorch==1.11
• pytorch-cuda=11.7
• torchvision=0.12

Troubleshooting

Visit: troubleshooting