This shows you the differences between two versions of the page.
Both sides previous revision Previous revision Next revision | Previous revision Next revision Both sides next revision | ||
downloads:cryolo_1 [2019/05/17 08:22] twagner [crYOLO] |
downloads:cryolo_1 [2019/07/09 19:49] twagner [Installation] |
||
---|---|---|---|
Line 12: | Line 12: | ||
You can find more technical details in our paper: | You can find more technical details in our paper: | ||
+ | Nature Communications Biology: | ||
+ | [[https:// | ||
+ | |||
+ | Preprint: | ||
[[https:// | [[https:// | ||
Line 52: | Line 56: | ||
=== For cryo images === | === For cryo images === | ||
- | Number of datasets: 38 real, 10 simulated, 10 particle free datasets on various grids with contaminations | + | Number of datasets: 38 real, 10 simulated, 10 particle free datasets on various grids with contamination |
Uploaded: 17. May 2019 | Uploaded: 17. May 2019 | ||
Line 98: | Line 102: | ||
* < | * < | ||
* < | * < | ||
- | * Issue 21: The search range for filament tracing is too low for many datasets. To check if you are affected: Use your trained model and pick without the filament options. Check if your filaments a nicely picked (many consecutive boxes on a filament). In the next version, the search range will be increased and added as an optional parameter. | + | * <del>Issue 21: The search range for filament tracing is too low for many datasets. To check if you are affected: Use your trained model and pick without the filament options. Check if your filaments a nicely picked (many consecutive boxes on a filament). In the next version, the search range will be increased and added as an optional parameter.</ |
- | * Issue 22: If absolute paths are used in the field " | + | * <del>Issue 22: If absolute paths are used in the field " |
Line 125: | Line 129: | ||
After that, create a new virtual environment: | After that, create a new virtual environment: | ||
< | < | ||
- | conda create -n cryolo -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 | + | conda create -n cryolo -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 |
</ | </ | ||
Line 135: | Line 139: | ||
Install crYOLO: | Install crYOLO: | ||
< | < | ||
- | conda install numpy==1.14.5 | + | conda install numpy==1.15.4 |
- | pip install cryolo-X.Y.Z.tar.gz | + | #IN CASE YOU WANT TO INSTALL THE GPU VERSION: |
+ | pip install cryolo-X.Y.Z.tar.gz[gpu] | ||
+ | #IN CASE YOU WANT TO INSTALL THE CPU VERSION: | ||
+ | pip install cryolo-X.Y.Z.tar.gz[cpu] | ||
pip install cryoloBM-X.Y.Z.tar.gz | pip install cryoloBM-X.Y.Z.tar.gz | ||
</ | </ | ||
Line 164: | Line 172: | ||
**crYOLO 1.3.6:** | **crYOLO 1.3.6:** | ||
* Changed filament search radius factor from 0.8 to 1.41 (this fixed issue 21) | * Changed filament search radius factor from 0.8 to 1.41 (this fixed issue 21) | ||
- | * Add search radius factor as parameter (-sr) during prediction in filament mode | + | * Add search radius factor as [[pipeline: |
* Improved error message in case of corrupted config file | * Improved error message in case of corrupted config file | ||
* Fixed issue 22: If absolute paths are used in the field “train_image” in your configuration file, filtering is skipped. | * Fixed issue 22: If absolute paths are used in the field “train_image” in your configuration file, filtering is skipped. |