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cryolo_archive [2018/12/20 15:23]
twagner [General model YOLO patched mode]
cryolo_archive [2019/09/20 08:34]
twagner [General PhosaursNet model]
Line 2: Line 2:
  
 ==== crYOLO ==== ==== crYOLO ====
 +No longer maintained. See pip archive
 +https://pypi.org/project/cryolo/#history
  
-=== Version: 1.2.0 === 
  
-Uploaded 27. November 2018 [[ftp://ftp.gwdg.de/pub/misc/sphire/crYOLO_V1_2_0/cryolo-1.2.0.tar.gz|DOWNLOAD]]+<hidden> 
 +**Version: 1.3.6**
  
 +Uploaded:  17. May 2019 [[ftp://ftp.gwdg.de/pub/misc/sphire/crYOLO_V1_3_6/cryolo-1.3.6.tar.gz|DOWNLOAD GPU VERSION]] [[ftp://ftp.gwdg.de/pub/misc/sphire/crYOLO_V1_3_6/cryolo-1.3.6.dev0.tar.gz|DOWNLOAD CPU VERSION]]
 +
 +**Version: 1.3.5**
 +
 +Uploaded:  03. May 2019 [[ftp://ftp.gwdg.de/pub/misc/sphire/crYOLO_V1_3_5/cryolo-1.3.5.tar.gz|DOWNLOAD GPU VERSION]] [[ftp://ftp.gwdg.de/pub/misc/sphire/crYOLO_V1_3_5/cryolo-1.3.5.dev0.tar.gz|DOWNLOAD CPU VERSION]]
 +
 +**Version: 1.3.4**
 +
 +Uploaded:  23. April 2019 [[ftp://ftp.gwdg.de/pub/misc/sphire/crYOLO_V1_3_4/cryolo-1.3.4.tar.gz|DOWNLOAD GPU VERSION]] [[ftp://ftp.gwdg.de/pub/misc/sphire/crYOLO_V1_3_4/cryolo-1.3.4.dev0.tar.gz|DOWNLOAD CPU VERSION]]
 +
 +**Version: 1.3.3**
 +
 +Uploaded:  08. April 2019 [[ftp://ftp.gwdg.de/pub/misc/sphire/crYOLO_V1_3_3/cryolo-1.3.3.tar.gz|DOWNLOAD GPU VERSION]][[ftp://ftp.gwdg.de/pub/misc/sphire/crYOLO_V1_3_3/cryolo-1.3.3.dev0.tar.gz|DOWNLOAD CPU VERSION]]
 +
 +**Version: 1.3.2**
 +
 +Uploaded:  05. April 2019 [[ftp://ftp.gwdg.de/pub/misc/sphire/crYOLO_V1_3_2/cryolo-1.3.2.tar.gz|DOWNLOAD GPU VERSION]] [[ftp://ftp.gwdg.de/pub/misc/sphire/crYOLO_V1_3_2/cryolo-1.3.2.dev0.tar.gz|DOWNLOAD CPU VERSION]]
 +
 +**Version: 1.3.1**
 +
 +Uploaded:  18. March 2019 [[ftp://ftp.gwdg.de/pub/misc/sphire/crYOLO_V1_3_1/cryolo-1.3.1.tar.gz|DOWNLOAD]]
 +
 +**Version: 1.3.0**
 +
 +Uploaded:  14. March 2019 [[ftp://ftp.gwdg.de/pub/misc/sphire/crYOLO_V1_3_0/cryolo-1.3.0.tar.gz|DOWNLOAD]]
 +
 +**Version: 1.2.3**
 +
 +Uploaded:  12. February 2019 [[ftp://ftp.gwdg.de/pub/misc/sphire/crYOLO_V1_2_3/cryolo-1.2.3.tar.gz|DOWNLOAD]]
 +
 +**Version: 1.2.2**
 +
 +Uploaded:  21. December 2018 [[ftp://ftp.gwdg.de/pub/misc/sphire/crYOLO_V1_2_2/cryolo-1.2.2.tar.gz|DOWNLOAD]]
 +
 +**Version: 1.2.1**
 +
 +Uploaded:  05. December 2018 [[ftp://ftp.gwdg.de/pub/misc/sphire/crYOLO_V1_2_1/cryolo-1.2.1.tar.gz|DOWNLOAD]]
 +
 +**Version: 1.2.0**
 +
 +Uploaded:  27. November 2018 [[ftp://ftp.gwdg.de/pub/misc/sphire/crYOLO_V1_2_0/cryolo-1.2.0.tar.gz|DOWNLOAD]]
  
-=== Version: 1.1.4 ===+**Version: 1.1.4**
  
 Uploaded:  18. September 2018 [[ftp://ftp.gwdg.de/pub/misc/sphire/crYOLO_V1_1_4/cryolo-1.1.4.tar.gz|DOWNLOAD]] Uploaded:  18. September 2018 [[ftp://ftp.gwdg.de/pub/misc/sphire/crYOLO_V1_1_4/cryolo-1.1.4.tar.gz|DOWNLOAD]]
  
-=== Version: 1.1.3 ===+**Version: 1.1.3**
  
 Uploaded:  14. September 2018 [[ftp://ftp.gwdg.de/pub/misc/sphire/crYOLO_V1_1_3/cryolo-1.1.3.tar.gz|DOWNLOAD]] Uploaded:  14. September 2018 [[ftp://ftp.gwdg.de/pub/misc/sphire/crYOLO_V1_1_3/cryolo-1.1.3.tar.gz|DOWNLOAD]]
  
-=== Version: 1.1.2 ===+**Version: 1.1.2**
  
 Uploaded: 12. September 2018 [[ftp://ftp.gwdg.de/pub/misc/sphire/crYOLO_V1_1_2/cryolo-1.1.2.tar.gz|DOWNLOAD]] Uploaded: 12. September 2018 [[ftp://ftp.gwdg.de/pub/misc/sphire/crYOLO_V1_1_2/cryolo-1.1.2.tar.gz|DOWNLOAD]]
  
-=== Version: 1.1.1 === +**Version: 1.1.1** 
 Uploaded:  10. September 2018 [[ftp://ftp.gwdg.de/pub/misc/sphire/crYOLO_V1_1_1/cryolo-1.1.1.tar.gz|DOWNLOAD]] Uploaded:  10. September 2018 [[ftp://ftp.gwdg.de/pub/misc/sphire/crYOLO_V1_1_1/cryolo-1.1.1.tar.gz|DOWNLOAD]]
  
-===Version: 1.1.0===+**Version: 1.1.0**
  
 Uploaded: 23. August 2018 [[ftp://ftp.gwdg.de/pub/misc/sphire/crYOLO_V1_1_0/cryolo-1.1.0.tar.gz|DOWNLOAD]] Uploaded: 23. August 2018 [[ftp://ftp.gwdg.de/pub/misc/sphire/crYOLO_V1_1_0/cryolo-1.1.0.tar.gz|DOWNLOAD]]
  
-===Version: 1.0.4===+**Version: 1.0.4**
  
 Uploaded:  13. July 2018 [[ftp://ftp.gwdg.de/pub/misc/sphire/crYOLO_V1_0_4/cryolo-1.0.4.tar.gz|DOWNLOAD]] Uploaded:  13. July 2018 [[ftp://ftp.gwdg.de/pub/misc/sphire/crYOLO_V1_0_4/cryolo-1.0.4.tar.gz|DOWNLOAD]]
  
-=== Version: 1.0.3 ===+**Version: 1.0.3**
  
 Uploaded:  09. July 2018 [[ftp://ftp.gwdg.de/pub/misc/sphire/crYOLO_V1_0_3/cryolo-1.0.3.tar.gz|DOWNLOAD]] Uploaded:  09. July 2018 [[ftp://ftp.gwdg.de/pub/misc/sphire/crYOLO_V1_0_3/cryolo-1.0.3.tar.gz|DOWNLOAD]]
  
-=== Version: 1.0.2 ===+**Version: 1.0.2**
  
 Uploaded:  04. July 2018 [[ftp://ftp.gwdg.de/pub/misc/sphire/crYOLO_V1_0_2/cryolo-1.0.2.tar.gz|DOWNLOAD]] Uploaded:  04. July 2018 [[ftp://ftp.gwdg.de/pub/misc/sphire/crYOLO_V1_0_2/cryolo-1.0.2.tar.gz|DOWNLOAD]]
  
-=== Version 1.0.1 ===+**Version 1.0.1**
  
 Download the **crYOLO version 1.0.1** here : [[ftp://ftp.gwdg.de/pub/misc/sphire/crYOLO_V1_0_1/cryolo-1.0.1.tar.gz|DOWNLOAD]] (UPDATED at 03. July 2018) Download the **crYOLO version 1.0.1** here : [[ftp://ftp.gwdg.de/pub/misc/sphire/crYOLO_V1_0_1/cryolo-1.0.1.tar.gz|DOWNLOAD]] (UPDATED at 03. July 2018)
  
-=== Version 1.0.0 ===+**Version 1.0.0**
  
 Download the **crYOLO version 1.0.0** here : [[ftp://ftp.gwdg.de/pub/misc/sphire/crYOLO_V1_0_0/cryolo-1.0.0.tar.gz|DOWNLOAD]] Download the **crYOLO version 1.0.0** here : [[ftp://ftp.gwdg.de/pub/misc/sphire/crYOLO_V1_0_0/cryolo-1.0.0.tar.gz|DOWNLOAD]]
  
- +</hidden>
-----+
  
 ==== crYOLO boxmanager ==== ==== crYOLO boxmanager ====
  
-=== Version: 1.0.4 ===+No longer maintained. See pip archive 
 +https://pypi.org/project/cryoloBM/#history 
 +<hidden> 
 +**Version: 1.2.2 ** 
 + 
 +Uploaded: 03. May 2019 [[ftp://ftp.gwdg.de/pub/misc/sphire/crYOLO_BM_V1_2_2/cryoloBM-1.2.2.tar.gz|DOWNLOAD]] 
 + 
 +** Version: 1.2.1 ** 
 + 
 +Uploaded: 05. April 2019 [[ftp://ftp.gwdg.de/pub/misc/sphire/crYOLO_BM_V1_2_1/cryoloBM-1.2.1.tar.gz|DOWNLOAD]] 
 + 
 +** Version: 1.2.0 ** 
 + 
 +Uploaded: 14. March 2019 [[ftp://ftp.gwdg.de/pub/misc/sphire/crYOLO_BM_V1_2/cryoloBM-1.2.tar.gz|DOWNLOAD]] 
 + 
 +** Version: 1.1.1 ** 
 + 
 +Uploaded: 21. December 2018 [[ftp://ftp.gwdg.de/pub/misc/sphire/crYOLO_BM_V1_1_1/cryoloBM-1.1.1.tar.gz|DOWNLOAD]] 
 + 
 +** Version: 1.1.0 ** 
 + 
 +Uploaded: 27. November 2018 [[ftp://ftp.gwdg.de/pub/misc/sphire/crYOLO_BM_V1_1_0/cryoloBM-1.1.0.tar.gz|DOWNLOAD]] 
 + 
 + 
 +** Version: 1.0.4 **
  
 Uploaded: 18. September 2018 [[ftp://ftp.gwdg.de/pub/misc/sphire/crYOLO_BM_V1_0_4/cryoloBM-1.0.4.tar.gz|DOWNLOAD]] Uploaded: 18. September 2018 [[ftp://ftp.gwdg.de/pub/misc/sphire/crYOLO_BM_V1_0_4/cryoloBM-1.0.4.tar.gz|DOWNLOAD]]
  
  
-=== Version: 1.0.3 ===+** Version: 1.0.3 **
  
 Uploaded: 23. August 2018 [[ftp://ftp.gwdg.de/pub/misc/sphire/crYOLO_BM_V1_0_3/cryoloBM-1.0.3.tar.gz|DOWNLOAD]] Uploaded: 23. August 2018 [[ftp://ftp.gwdg.de/pub/misc/sphire/crYOLO_BM_V1_0_3/cryoloBM-1.0.3.tar.gz|DOWNLOAD]]
  
-=== Version: 1.0.2 ===+** Version: 1.0.2 **
  
 Uploaded: 09. July 2018 [[ftp://ftp.gwdg.de/pub/misc/sphire/crYOLO_BM_V1_0_2/cryoloBM-1.0.2.tar.gz|DOWNLOAD]] Uploaded: 09. July 2018 [[ftp://ftp.gwdg.de/pub/misc/sphire/crYOLO_BM_V1_0_2/cryoloBM-1.0.2.tar.gz|DOWNLOAD]]
  
-=== Version: 1.0.1 ===+** Version: 1.0.1 **
  
 Uploaded: 03. July 2018 [[ftp://ftp.gwdg.de/pub/misc/sphire/crYOLO_V1_0_1/cryoloBM-1.0.1.tar.gz|DOWNLOAD]] Uploaded: 03. July 2018 [[ftp://ftp.gwdg.de/pub/misc/sphire/crYOLO_V1_0_1/cryoloBM-1.0.1.tar.gz|DOWNLOAD]]
  
-=== Version 1.0.0 === +** Version 1.0.0 **
 Download the **crYOLO boxmanager 1.0.0** here: [[ftp://ftp.gwdg.de/pub/misc/sphire/crYOLO_V1_0_0/cryoloBM-1.0.0.tar.gz|DOWNLOAD]] Download the **crYOLO boxmanager 1.0.0** here: [[ftp://ftp.gwdg.de/pub/misc/sphire/crYOLO_V1_0_0/cryoloBM-1.0.0.tar.gz|DOWNLOAD]]
 +</hidden>
 +
 +==== General PhosaursNet model ===
 +
 +=== Version 20190516 ===
 +38 real, 10 simulated, 10 particle free datasets on various grids with contamination
 +
 +cryo (low-pass): [[ftp://ftp.gwdg.de/pub/misc/sphire/crYOLO-GENERAL-MODELS/gmodel_phosnet_20190516.h5
 +|DOWNLOAD]] 
 +
 +Config is the same as in version 20191221. 
 +
 +cryo (janni): [[ftp://ftp.gwdg.de/pub/misc/sphire/crYOLO-GENERAL-MODELS/gmodel_phosnet_201907_nn_denoise.h5
 +|DOWNLOAD]] 
 +<code .json>
 +    {
 +    "model" : {
 +        "architecture":         "PhosaurusNet",
 +        "input_size":           1024,
 +        "anchors":              [205,205],
 +        "max_box_per_image":    700,
 +        "num_patches":          1,
 +        "filter":               ["gmodel_janni_20190703.h5",24,3,"tmp_filtered_nn"]
 +      }
 +    }
 +</code>
 +
 +=== Version 20190314 ===
 +
 +[[ftp://ftp.gwdg.de/pub/misc/sphire/crYOLO-GENERAL-MODELS/gmodel_phosnet_20190314.h5
 +|DOWNLOAD]] (Uploaded: 14. March 2019) Number of datasets: 32 real, 10 simulated, 10 particle free datasets on various grids with contaminations.
 +
 +Config is the same as in version 20191221.
 +
 +=== Version 20190218 ===
 +
 +[[ftp://ftp.gwdg.de/pub/misc/sphire/crYOLO-GENERAL-MODELS/gmodel_phosnet_20190218_loss0042.h5 |DOWNLOAD]] (Uploaded: 18. February 2019) Number of datasets: 30 real, 10 simulated, 10 particle free datasets on various grids with contaminations
 +
 +Config is the same as in version 20191221.
  
 +=== Version 20191221 ===
  
-----+[[ftp://ftp.gwdg.de/pub/misc/sphire/crYOLO-GENERAL-MODELS/gmodel_phosnet_20181221_loss0037.h5 
 +|DOWNLOAD]] (Uploaded: 21. December 2018)  Number of datasets: 27 (real), 10 simulated, 10 particle free datasets on various grids
  
 +<code json config.json>
 +    {
 +    "model" : {
 +        "architecture":         "PhosaurusNet",
 +        "input_size":           1024,
 +        "anchors":              [205,205],
 +        "max_box_per_image":    700,
 +        "num_patches":          1,
 +        "filter":               [0.1,"tmp_filtered"]
 +      }
 +    }
 +</code>
  
 ==== General model YOLO patched mode ==== ==== General model YOLO patched mode ====
Line 85: Line 204:
 [[ftp://ftp.gwdg.de/pub/misc/sphire/crYOLO-GENERAL-MODELS/gmodel_yolo_20181127_1100.h5|DOWNLOAD]] (Uploaded: 27. November 2018) Number of datasets: 27 (real), 10 simulated, 10 particle free datasets on various grids [[ftp://ftp.gwdg.de/pub/misc/sphire/crYOLO-GENERAL-MODELS/gmodel_yolo_20181127_1100.h5|DOWNLOAD]] (Uploaded: 27. November 2018) Number of datasets: 27 (real), 10 simulated, 10 particle free datasets on various grids
  
-[[pipeline:window:cryolo#configuration1 |Valid configuration file]+<code json config.json> 
- +
-InfoTrained on cryo imagestherefore negative stain will not work.+    "model" 
 +        "architecture"        "YOLO", 
 +        "input_size":           1024, 
 +        "anchors":              [205,205], 
 +        "overlap_patches":      200, 
 +        "max_box_per_image"   700, 
 +        "num_patches":          2, 
 +        "filter":               [0.1,"tmp_filtered"
 +    } 
 +
 +</code>
  
 === Version 20180823 === === Version 20180823 ===
cryolo_archive.txt · Last modified: 2019/10/15 16:41 by twagner