This plugin provides a wrapper for some programs of SPHIRE software suite:
JANNI (Just Another Noise 2 Noise Implementation): a neural network denoising tool
crYOLO: a fast and accurate particle picking procedure. It’s based on convolutional neural networks and utilizes the popular You Only Look Once (YOLO) object detection system.
Installation
You will need to use 3.0+ version of Scipion to be able to run these protocols. To install the plugin, you have two options:
Stable version
It can be installed in user mode via Scipion plugin manager (Configuration > Plugins) or using the command line:
scipion installp -p scipion-em-sphireDeveloper’s version
download repository
git clone -b devel https://github.com/scipion-em/scipion-em-sphire.gitinstall
scipion installp -p /path/to/scipion-em-sphire --devel
crYOLO software will be installed automatically with the plugin but you can also use an existing installation by providing CRYOLO_ENV_ACTIVATION (see below).
Important: you need to have conda (miniconda3 or anaconda3) pre-installed to use this program.
To check the installation you can run the plugin’s tests:
scipion test --grep sphire --run
Configuration variables
CONDA_ACTIVATION_CMD: If undefined, it will rely on conda command being in the PATH (not recommended), which can lead to execution problems mixing scipion python with conda ones. One example of this could can be seen below but depending on your conda version and shell you will need something different:
CONDA_ACTIVATION_CMD = eval “$(/extra/miniconda3/bin/conda shell.bash hook)”
CRYOLO_ENV_ACTIVATION (default = conda activate cryolo-1.9.9): Command to activate the crYOLO environment.
NAPARI_ENV_ACTIVATION (default = conda activate napari-0.4.17): Command to activate napari environment (used only for tomo picker viewer).
Downloaded crYOLO and JANNI general models can be found in the following locations:
<SCIPION_HOME>/software/em/cryolo_model-[model_version]
<SCIPION_HOME>/software/em/cryolo_negstain_model-[model_version] (not installed by default)
<SCIPION_HOME>/software/em/janni_model-[model_version]
Running on CPU
crYOLO can run on CPU, however this is only recommended for picking protocol and not training. For that reason the CPU implementation is only available for the crYOLO-Picking protocol.
The CPU implementation of crYOLO is not installed by default. Therefore you must install the cryoloCPU-[version] package in the Configuration > Plugins >> scipion-em-sphire or by running:
scipion installb cryoloCPU
The CPU version of crYOLO is installed under a separate conda environment called cryoloCPU-[version]. If you already have a cryoloCPU environment pre-installed, then modify the following variable in the Scipion config file:
CRYOLO_ENV_ACTIVATION_CPU = conda activate envName
Supported versions
1.9.3, 1.9.6, 1.9.7, 1.9.9
Protocols
import crYOLO training model
crYOLO picking
crYOLO tomo picking
crYOLO training
JANNI denoising
References
Wagner, T. et al. SPHIRE-crYOLO is a fast and accurate fully automated particle picker for cryo-EM. Communications Biology 2, (2019).
Release files for scipion-em-sphire 3.2.6
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| scipion_em_sphire-3.2.6.tar.gz | 50.1 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| scipion_em_sphire-3.2.6-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 117.7 kB
Release files / scipion_em_sphire-3.2.6.tar.gz
| Download URL | scipion_em_sphire-3.2.6.tar.gz |
|---|---|
| Size | 50.1 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
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Release files / scipion_em_sphire-3.2.6-py3-none-any.whl
| Download URL | scipion_em_sphire-3.2.6-py3-none-any.whl |
|---|---|
| Size | 67.6 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
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No |
| Uploaded via |
twine/6.1.0 CPython/3.8.18
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