scipion-em-sphire 1.2.9

Cryolo picker, training and custom model importer.

Sphire Scipion plugin

This plugin allows to use cryolo within Scipion framework. So far we have implemented:

• crYOLO particle picker (current version: 1.5.3)

This plugin will be able to install cryolo 1.5.3 and the generic model.

crYOLO is a pipeline for particle detection in cryo-electron microscopy images which is based on the deep learning object detection system “You Only Look Once” (YOLO).

Setup

Requires to have conda installed and not initialized in the shell.

For Users

Install Scipion2, follow the ‘crYOLO integration’ instructions below and install the cryolo plugin.

For developers

1. For testing and develop this plugin, you need to use the Scipion v2.0 in devel. For that, just install Scipion from GitHub, using the ‘devel’ branch.

2. Follow the ‘crYOLO integration’ instructions below.

3. Clone this repository in you system:

   cd
   git clone https://github.com/scipion-em/scipion-em-sphire

4. Install the sphire plugin in devel mode:

   scipion installp -p ~/scipion-em-sphire --devel

crYOLO integration

The following steps presuppose that you have Anaconda or Miniconda installed on your computer. In ~/.config/scipion/scipion.conf set CONDA_ACTIVATION_CMD variable in the Packages section.

For example:

CONDA_ACTIVATION_CMD = . ~/anaconda2/etc/profile.d/conda.sh

Notice the command starts with a period! This will source the conda.sh script. This is needed to activate the conda environment. For further information please visit the following website [here]

If you wish to install the plugin with the default settings just go to plugin manager and install scipion-em-sphire. This will create the default environment named cryolo and download version 1.4.0 for you.

You are ready to use crYOLO. If you wish to change the environment name you can introduce CRYOLO_ENV_ACTIVATION variable in the ~/.config/scipion.conf variables section:

For example:

CRYOLO_ENV_ACTIVATION = conda activate yourdesiredname

crYOLO general model is not installed by default. You may install it by expanding the plugin in the plugin manager and install it. This will install the general model to a default location: ~/scipion/software/em/cryolo_model-20190516.

If you wish to provide a different general model: Set CRYOLO_GENERIC_MODEL variable in the ~/.config/scipion.conf variables section:

For example:

CRYOLO_GENERIC_MODEL = /your/desired/location/myownmodelname.h5

Running crYOLO tests

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

scipion test --grep cryolo --run