IsoNet is a deep learning-based software package that iteratively reconstructs the missing-wedge information and increases signal-to-noise ratio, using the knowledge learned from raw tomograms. Without the need for sub-tomogram averaging, IsoNet generates tomograms with significantly reduced resolution anisotropy. Applications of IsoNet to three representative types of cryoET data demonstrate greatly improved structural interpretability: resolving lattice defects in immature HIV particles, establishing architecture of the paraflagellar rod in Eukaryotic flagella, and identifying heptagon-containing clathrin cages inside a neuronal synapse of cultured cells. detect AMR genes from thirteen genomes of Pseudomonas strains.

References:

• Yun-Tao Liu, Heng Zhang, Hui Wang, Chang-Lu Tao, Guo-Qiang Bi & Z. Hong Zhou
  Isotropic reconstruction for electron tomography with deep learning
  Nature Communications volume 13, Article number: 6482 (2022)
  

• IsoNet on Github

• Module Name: IsoNet (see the modules page for more information)
• Unusual environment variables set
  • ISONET_HOME  installation directory
  • ISONET_BIN       bin directory
  • ISONET_SRC       source directory

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive 
[user@cn3107 ~]$ module load IsoNet
[+] Loading singularity  3.10.5  on cn4183
[+] Loading CUDA Toolkit  10.2.89  ...
[+] Loading cuDNN/7.6.5/CUDA-10.2 libraries...
[+] Loading IsoNet  0.2.1
[user@cn3107 ~]$ isonet.py -h 
INFO: Showing help with the command 'isonet.py -- --help'.

NAME
    isonet.py - ISONET: Train on tomograms and restore missing-wedge

SYNOPSIS
    isonet.py -

DESCRIPTION
    for detail discription, run one of the following commands:

    isonet.py prepare_star -h
    isonet.py prepare_subtomo_star -h
    isonet.py deconv -h
    isonet.py make_mask -h
    isonet.py extract -h
    isonet.py refine -h
    isonet.py predict -h
    isonet.py resize -h
    isonet.py gui -h

[user@cn3107 ~]$ isonet.py gui 

[user@cn3107 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$