IsoNet plugin

This plugin allows to use IsoNet programs within the Scipion framework

IsoNet stand for ISOtropic reconstruction of Electron Tomography. It train deep neural networks to reconstruct meaningful contents in the missing wedge for electron tomography increase signal-to-noise ratio using the information learned from the original tomogram. The software requires tomograms as input. Observing at about 30A resolutions, the IsoNet generated tomograms are largely isotropic.

You will need to use 3.0.0 version of Scipion to run these protocols.

Protocols

• Isotropic Reconstruction: Isotropic Reconstruction of Electron Tomograms with Deep Learning

Latest plugin version

v3.0.2

• fixed : Validated gcc version
• fixed : Fixed an error related with cuda lib

v3.0.1

• new : Isotropic Reconstruction

v3.0.0

• new : First plugin version

Installing the plugin

In order to install the plugin follow these instructions:

1. Install the plugin

scipion installp -p scipion-em-isonet

or through the plugin manager by launching Scipion and following Configuration >> Plugins

To install in development mode

• Clone or download the plugin repository

git clone https://github.com/scipion-em/scipion-em-isonet.git

• Install the plugin in developer mode.

scipion installp -p local/path/to/scipion-em-isonet --devel

Configuration variables

There are some optional variables related to the IsoNet plugin installation. For example, if you have installed IsoNet outside of Scipion, you may define ISONET_HOME in your scipion.conf file for specifying an already existing IsoNet installation path. Note that a directory called IsoNet is expected to exist within this path (create a link if necessary):

ISONET_HOME = /path/to/my/own/isonet/install/

In the above example, the directory /path/to/my/own/isonet/install/IsoNet should exist for the plugin to work.

Also, you can use the ISONET_ACTIVATION_CMD environment variable to indicate an activation command for IsoNet, which can be a conda environment or anything else (e.g. sourcing a script):

ISONET_ACTIVATION_CMD = conda activate my-isonet-env

If these variables are not defined, default values will be used that will work with the latest version installed through Scipion.

Buildbot status

Status devel version:

Status production version:

IsoNet References

The publication associated with IsoNet can be found here: