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downloads:cryolo_1 [2019/10/07 16:13]
twagner [Installation]
downloads:cryolo_1 [2020/05/25 10:14] (current)
twagner
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 {{ :​downloads:​cryolo_logo.jpg?​600 |}} {{ :​downloads:​cryolo_logo.jpg?​600 |}}
 +<note important>​
 +
 +**DOCUMENTATION OUTDATED**
 +
 +The documentation has moved to https://​cryolo.readthedocs.io/​en/​latest/​
 +
 +</​note>​
 +
 ====== License ====== ====== License ======
  
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 You can find more technical details in our paper: You can find more technical details in our paper:
  
-Nature ​Communications Biology:+Communications Biology:
 [[https://​doi.org/​10.1038/​s42003-019-0437-z|SPHIRE-crYOLO is a fast and accurate fully automated particle picker for cryo-EM]] [[https://​doi.org/​10.1038/​s42003-019-0437-z|SPHIRE-crYOLO is a fast and accurate fully automated particle picker for cryo-EM]]
  
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 ====crYOLO==== ====crYOLO====
  
-Version: 1.5.3+Version: 1.6.1
  
-Uploaded: ​ 30. September 2019+Uploaded: ​ 30. March 2020
  
 [[https://​pypi.org/​project/​cryolo/#​files|DOWNLOAD]] [[https://​pypi.org/​project/​cryolo/#​files|DOWNLOAD]]
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 ====crYOLO boxmanager==== ====crYOLO boxmanager====
  
-Version: 1.2.7+Version: 1.3.5
  
-Uploaded: ​26September 2019+Uploaded: ​22March 2020
  
 [[https://​pypi.org/​project/​cryoloBM/#​files|DOWNLOAD]] [[https://​pypi.org/​project/​cryoloBM/#​files|DOWNLOAD]]
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 === For cryo images (low-pass filtered) === === For cryo images (low-pass filtered) ===
-Number of datasets: ​40 real, 10 simulated, 10 particle free datasets on various grids with contamination+Number of datasets: ​43 real, 10 simulated, 10 particle free datasets on various grids with contamination
  
-Uploaded: ​20September 2019+Uploaded: ​16March 2020
  
-[[ftp://​ftp.gwdg.de/​pub/​misc/​sphire/​crYOLO-GENERAL-MODELS/​gmodel_phosnet_201909.h5+[[ftp://​ftp.gwdg.de/​pub/​misc/​sphire/​crYOLO-GENERAL-MODELS/​gmodel_phosnet_202002_N63.h5
 |DOWNLOAD]] ​ |DOWNLOAD]] ​
  
 === For cryo images (neural network denoised with JANNI) === === For cryo images (neural network denoised with JANNI) ===
-Number of datasets: ​40 real, 10 simulated, 10 particle free datasets on various grids with contamination+Number of datasets: ​43 real, 10 simulated, 10 particle free datasets on various grids with contamination
  
-Uploaded: ​20September 2019+Uploaded: ​17March 2020
  
-[[ftp://​ftp.gwdg.de/​pub/​misc/​sphire/​crYOLO-GENERAL-MODELS/​gmodel_phosnet_201909_nn_denoise.h5+[[ftp://​ftp.gwdg.de/​pub/​misc/​sphire/​crYOLO-GENERAL-MODELS/​gmodel_phosnet_202003_nn_N63.h5
 |DOWNLOAD]] ​ |DOWNLOAD]] ​
  
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 ====== Installation ====== ====== Installation ======
 +
 +<note important>​
 +
 +**DOCUMENTATION OUTDATED**
 +
 +The documentation has moved to https://​cryolo.readthedocs.io/​en/​latest/​
 +
 +</​note>​
  
 **System requirements:​** **System requirements:​**
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 </​note>​ </​note>​
  
- +{{page>pipeline:window:cryolo:issues}}
-<note important> +
-**Known issues** +
- +
-  * Issue 0Training on multiple GPUs sometimes lead to worse performance (higher loss). We currently recommend to train on single gpus. +
-  * Issue 17On the fly filtering (%%--%%otf) is slower than using it not, as the filtering is not parallelized in this case.  +
-  * Issue 26If you select filtering "​None"​ crYOLO does not train properly. +
- +
- +
- +
-<hidden Closed ​issues+
-  * <​del> ​ Issue 1: crYOLO sometimes not exit properly after training finished. Has to be killed manually.</​del>​ +
-  * <​del>​Issue 2: If you use automatic filtering with .tif files, you get an error like "​OSError:​ cannot identify image file '​filtered_folder/​another_folder/​my_image.tif'"​. It will be fixed in the next release.</​del>​ +
-  * <​del>​Issue 3: (Boxmanager) The visualization only shows the first filament when loading eman1 helical box files (start end coordinates). Will be fixed in the next release.</​del>​ +
-  * <​del>​Issue 4: The filament mode will crash if crYOLO cannot identify a single particle in the image. Will be fixed in 1.2.2</​del>​ +
-  * <​del>​Issue 5: If movies were aligned with cisTEM and picked with crYOLO, the box position are vertically flipped. Will be fixed in 1.2.2</​del>​ +
-  * <​del>​Issue 6: crYOLO does overwrite the environmental variable "​CUDA_VISIBLE_DEVICES"​ with 0 if no gpu is specified by the -g parameter. This leads to the behavior that crYOLO ignores previous settings in CUDA_VISIBLE_DEVICES. Will be fixed in 1.2.2</​del>​ +
-  * <​del>​Issue 7: On K3 images crYOLO seems to add a offset toward the longer axis of the input image.</​del>​ +
-  * <​del>​Issue 8: There is a logical error in filament tracing, which sometimes connects two parallel filaments.</​del>​ +
-  * <​del>​Issue 9: Some people report an error when running cryolo prediction/​training:​ "​ImportError:​ numpy.core.multiarray failed to import"​. It will be fixed in 1.2.3.</​del>​ +
-  * <​del>​Issue 10: On machines with many cores (e.g 64) an error during filtering might pop up: "​[ERROR:​0] 53: Can't spawn new thread"</​del>​ +
-  * <​del>​Issue 11: If the -g parameter is not provided, crYOLO will use the memory of all GPUs. Will be fixed in 1.2.3.</​del>​ +
-  * <​del>​Issue 12: The LineEnhancer depdenceny of crYOLO is still dependent from opencv. Workaround: In the crYOLO environment:​ conda install opencv</​del>​ +
-  * <​del>​Issue 13: After picking it can happen that some of the boxes are not fully immersed in the image. Will be fixed in 1.2.4.</​del>​ +
-  * <​del>​Issue 14: Parallelization in filament mode is broken. Will be fixed in 1.2.4.</​del>​ +
-  * <​del>​Issue 15: If the %%--%%gpu_fraction is used, crYOLO always uses GPU 0. Will be fixed in 1.3.1.</​del>​  +
-  * <​del>​Issue 16: %%--%%gpu_fraction only works for prediction, not for training. Will be fixed in 1.3.2.</​del>​ +
-  * <​del>​Issue 18: Prediction is broken in 1.3.2. It removes all particles as it claim they are not fully immersed in the image.</​del>​ +
-  * <​del>​Issue 19: Filtering does not work if target image directory is absolute path.</​del>​ +
-  * <​del>​Issue 20: crYOLO 1.3.4 has a normalization bug. During training the images are normalized seperately, but during prediction is done batch wise. Workaround: Use -pbs 1 during prediction. It will be fixed in 1.3.5.</​del>​ +
-  * <​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.</​del>​ +
-  * <​del>​Issue 22: If absolute paths are used in the field "​train_image"​ in your configuration file, filtering is skipped.</​del>​ +
-  * <​del>​Issue 23: Since crYOLO 1.4.0 it sometimes take long until it starts picking. The reason seems to be the tensorflow update.<​del>​ +
-  * <​del>​Issue 24: Fine-tune mode does not start (cannot find layer model_3). Will be fixed in 1.4.1.<​del>​ +
-  * <​del>​Issue 25: When using GUI, prediction behaves differently than using command line. The reason is, that it uses a different multiprocessing start method. Will be fixed with 1.5.1</​del>​ +
-</​hidden>​ +
-</​note>​ +
 **That'​s it!** **That'​s it!**
  
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 {{page>​pipeline:​window:​cryolo:​changelog}} {{page>​pipeline:​window:​cryolo:​changelog}}
 ====crYOLO Boxmanager==== ====crYOLO Boxmanager====
-**crYOLO Boxmanager ​Version ​1.2.6:** + 
-  * Make it compatible ​with current new environment+**crYOLO Boxmanager 1.3.5** 
 +  * Fixed a bug when placing, moving or deleting a box 
 +  * Fixed bug of nun closing progress dialog when writing boxfiles 
 + 
 +**crYOLO Boxmanager 1.3.1** 
 +  * Speed up boxfile import is now 2x faster compared to 1.3.0. 
 +  * Big speed-up for live-preview during filtering. Should now even work with very big datasets. 
 + 
 + 
 +**crYOLO Boxmanager 1.3.0** 
 +  * Added option to plot size- and confidence distribution for cbox files. 
 +  * Added slider to filter particles according their estimated size. 
 +  * Added addition field for the number of boxes with live update. 
 +  * Added wildcard commandline option. 
 +  * Show progress-bar when reading and writing box-files. 
 +  * Various speed-ups.
  
 <hidden **Old crYOLO Boxmanager change logs**> <hidden **Old crYOLO Boxmanager change logs**>
 +
 +**crYOLO Boxmanager Version 1.2.9:**
 +  * Fixed a problem that only one filament is shown
 +
 +**crYOLO Boxmanager Version 1.2.8:**
 +  * Add a low pass filter
 +
 +**crYOLO Boxmanager Version 1.2.6:**
 +  * Make it compatible with current new environment
  
 **crYOLO Boxmanager Version 1.2.3:** **crYOLO Boxmanager Version 1.2.3:**
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 </​hidden>​ </​hidden>​
 ==== General PhosaurusNet model ==== ==== General PhosaurusNet model ====
-**Version ​20190516:**:+ 
 +**Version ​202002:** 
 +  * Adjusted the training data that the box sizes better reflect the particle diameter. 
 + 
 +**Version 201912:** 
 +  * Added two more datasets. 
 + 
 +**Version 20190516:**
   * Added four more inhouse datasets   * Added four more inhouse datasets
   * Added SNRNP (Thanks to Clement Charenton) ​   * Added SNRNP (Thanks to Clement Charenton) ​
  • downloads/cryolo_1.1570457610.txt.gz
  • Last modified: 2019/10/07 16:13
  • by twagner