This plugin provides wrappers for several programs of SPIDER software suite.
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
scipion installp -p scipion-em-spiderDeveloper’s version
download repository
git clone -b devel https://github.com/scipion-em/scipion-em-spider.gitinstall
scipion installp -p /path/to/scipion-em-spider --devel
SPIDER binaries will be installed automatically with the plugin, but you can also link an existing installation. Default installation path assumed is software/em/spider-26.06, if you want to change it, set SPIDER_HOME in scipion.conf file to the folder where the SPIDER is installed. Additional information about using SPIDER with MPI can be found on a separate page. Unfortunately, at the moment we do not support MPI in our SPIDER wrappers, since it requires a lot of effort to refactor almost all protocols. :( Depending on you CPU type you might want to change the default binary from spider_linux_mp_intel64 to a different one by explicitly setting SPIDER variable.
To check the installation, simply run one of the following Scipion tests:
scipion test spider.tests.test_protocols_spider_reconstruct.TestSpiderReconstruct
scipion test spider.tests.test_protocols_spider_align.TestSpiderAlign
scipion test spider.tests.test_workflow_spiderMDA.TestSpiderWorkflow
scipion test spider.tests.test_workflow_spiderMDA.TestSpiderConvert
scipion test spider.tests.test_protocols_spider_projmatch.TestSpiderRefinementA complete list of tests can also be seen by executing scipion test --show --grep spider
Supported versions
26.06
Protocols
Custom 2D mask
Filter particles
Reconstruct Fourier
Refinement
References
J. Frank et al. (1996). SPIDER and WEB: Processing and visualization of images in 3D electron microscopy and related fields. JSB. 116: 190-199.
2 maintainers
Metadata
2 maintainers
Release files for scipion-em-spider 3.1.8
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_spider-3.1.8.tar.gz | 110.6 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| scipion_em_spider-3.1.8-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 271.7 kB
Release files / scipion_em_spider-3.1.8.tar.gz
| Download URL | scipion_em_spider-3.1.8.tar.gz |
|---|---|
| Size | 110.6 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
e26886a8dd466e90622ef02b99451ea043786515cb0e6c651f9d6e85b8679689
|
|
BLAKE2b-256 checksum How to use checksums |
cea3e7cc187a743551645cacf7e56d99305ad297fe33de76abeba8c65f066d87
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.1.0 CPython/3.8.18
|
Release files / scipion_em_spider-3.1.8-py3-none-any.whl
| Download URL | scipion_em_spider-3.1.8-py3-none-any.whl |
|---|---|
| Size | 161.1 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
29bd16a2914b303fe07647ca5d9817ff7d2e0c7da106155c2fb1dacbcfb3e3a6
|
|
BLAKE2b-256 checksum How to use checksums |
de907205c98a1fa77aaed9ce92e423bdbfcd8d46b9489d023077be4a77963edf
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.1.0 CPython/3.8.18
|
