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Plugin to use the denoising functionality of Sphire-Janni program within the Scipion framework.

Project description

JANNI Scipion Plugin

This plugin allows to use the denoising functionality of Sphire-Janni software within Scipion framework. It installs Janni and downloads the generic pre-trained model.

NOTE: this version is not streamified and does not process in batches.

JANNI (Just Another Noise 2 Noise Implementation) implements a neural network denoising tool described.

Setup

It is assumed that Scipion is currently installed. If not, follow the instructions here.

Janni plugin requires to have Conda (Anaconda or Miniconda) installed and not initialized in the shell.

  • Install this plugin in user mode:

    It can be installed in user mode via Scipion main window (Configuration > Plugins) or using the command line:

scipion installp -p local/path/to/scipion-em-janni
  • Install this plugin in developer mode:

    Using the command line:

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

JANNI integration

The following steps presuppose that you have Anaconda or Miniconda installed on your computer. In $SCIPION_HOME/config/scipion.conf (Option View > Show Hidden Files must be enabled) set CONDA_ACTIVATION_CMD variable in the Packages section.

For example:

CONDA_ACTIVATION_CMD = . ~/anaconda3/etc/profile.d/conda.sh

Running JANNI tests

To check that everything is properly installed and configured, you might want to run some tests:

scipion test --grep janni --run

Project details


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Files for scipion-em-janni, version 1.0.1
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