This plugin implements protocols from the MemBrain family of software packages for analysis of membrane proteins in cryo-electron tomography.
Installation
The plugin is currently only available in development mode. To install, proceed with the following steps:
Clone this repo:
git clone https://github.com/scipion-em/scipion-em-membrain.gitInstall this plugin in devel (editable) mode:
scipion3 installp -p /path/to/scipion-em-membrain --develScipion will automatically install MemBrain and download any pre-trained models necessary for running it.
Configuration variables
There are some optional variables related to the MemBrain installation. For example, if you have installed MemBrain-seg outside of Scipion, you may define MEMBRAIN_SEG_ENV_ACTIVATION in your scipion.conf file for specifying an already existing conda environment or a script to be sourced:
MEMBRAIN_SEG_ENV_ACTIVATION = conda activate my-membrain-seg-envAlso, you can use the MEMBRAIN_SEG_MODEL environment variable to indicate the full path to a MemBrain-seg model downloaded externally:
MEMBRAIN_SEG_MODEL = /path/to/membrain-seg/model.ckptIf these variables are not defined, default values will be used that will work with the latest version installed through Scipion.
Protocols
The following protocols are currently implemented:
Membrane segmentation using the MemBrain-seg module
Using GPU or CPU
By default, MemBrain protocols assume that a GPU card is available. If such a device is not found, protocols may still run using the CPU with parallel threads, but will be much slower.
References
<!– in JSB citation style: –>
Lamm, L., Zufferey, S., Righetto, R.D., Wietrzynski, W., Yamauchi, K.A., Burt, A., Liu, Y., Zhang, H., Martinez-Sanchez, A., Ziegler, S., Isensee, F., Schnabel, J.A., Engel, B.D., Peng, T., 2024. MemBrain v2: an end-to-end tool for the analysis of membranes in cryo-electron tomography. https://doi.org/10.1101/2024.01.05.574336
Lamm, L., Righetto, R.D., Wietrzynski, W., Pöge, M., Martinez-Sanchez, A., Peng, T., Engel, B.D., 2022. MemBrain: A deep learning-aided pipeline for detection of membrane proteins in Cryo-electron tomograms. Computer Methods and Programs in Biomedicine 224, 106990. https://doi.org/10.1016/j.cmpb.2022.106990
Contact information
If you experiment any problem, please contact us here: scipion-users@lists.sourceforge.net or open an issue.
We’ll be pleased to help.
Scipion Team
1 maintainer
Metadata
1 maintainer
Release files for scipion-em-membrain 3.1.5
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_membrain-3.1.5.tar.gz | 89.7 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| scipion_em_membrain-3.1.5-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 180.8 kB
Release files / scipion_em_membrain-3.1.5.tar.gz
| Download URL | scipion_em_membrain-3.1.5.tar.gz |
|---|---|
| Size | 89.7 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
172b071f79968c6a0c3bf6d16e6780b4f1df7df0cf6b6750267fa7b166da0d1f
|
|
BLAKE2b-256 checksum How to use checksums |
d688a040b7f77ca7bd484e6bdc98f9722f396f768fd45fa3d1b12e70df047198
|
| 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_membrain-3.1.5-py3-none-any.whl
| Download URL | scipion_em_membrain-3.1.5-py3-none-any.whl |
|---|---|
| Size | 91.1 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
3b0fb0d6752e1f116223a1bf8232ac25a7255d8e75e5b65fada1aab6596bad55
|
|
BLAKE2b-256 checksum How to use checksums |
8a417a6227740e60ce1cf0364d937f516b746d400d06d54185cebbd5ee133815
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.1.0 CPython/3.8.18
|
