DeepLearningToolkit

The DeepLearningToolkit 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)

How to install

Run scipion3 installb deepLearningToolkit

It could take more than 30 minutes. To speedup the installation (we experienced a x4 speedup) we propose to use libmamba solver. 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 https://github.com/I2PC/xmipp/wiki/DeepLearningToolkit-troubleshooting