pipeline:window:cryolo
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pipeline:window:cryolo [2019/03/18 14:58] twagner [Picking particles - Without training using a general model] |
pipeline:window:cryolo [2019/05/17 08:25] twagner [Advanced parameters] |
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| * crYOLO makes picking **smart** -- The network learns the context of particles (e.g. not to pick particles on carbon or within ice contamination ) | * crYOLO makes picking **smart** -- The network learns the context of particles (e.g. not to pick particles on carbon or within ice contamination ) | ||
| * crYOLO makes training **easy** -- You might use a general network model and skip training completely. However, if the general model doesn' | * crYOLO makes training **easy** -- You might use a general network model and skip training completely. However, if the general model doesn' | ||
| - | * crYOLO makes training **lenient** -- Don't worry if you miss quite a lot particles during creation of your training set. [[: | + | * crYOLO makes training **tolerant** -- Don't worry if you miss quite a lot particles during creation of your training set. [[: |
| In this tutorial we explain our recommended configurations for single particle and filament projects. You can find more information about supported networks and about the config file in the following articles: | In this tutorial we explain our recommended configurations for single particle and filament projects. You can find more information about supported networks and about the config file in the following articles: | ||
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| Create a new directory called '' | Create a new directory called '' | ||
| - | Now create a third folder with the name '' | + | Now create a third folder with the name '' |
| ==== Configuration ==== | ==== Configuration ==== | ||
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| " | " | ||
| " | " | ||
| - | " | + | " |
| " | " | ||
| " | " | ||
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| to the training command. | to the training command. | ||
| ==== Picking ==== | ==== Picking ==== | ||
| - | You can now use the model weights saved in '' | + | You can now use the model weights saved in '' |
| < | < | ||
| cryolo_predict.py -c config.json -w model.h5 -i full_data/ -g 0 -o boxfiles/ | cryolo_predict.py -c config.json -w model.h5 -i full_data/ -g 0 -o boxfiles/ | ||
| </ | </ | ||
| - | You will find the picked particles in the directory '' | + | You will find the picked particles in the directory '' |
| If you want to pick less conservatively or more conservatively you might want to change the selection threshold from the default of 0.3 to a less conservative value like 0.2 or more conservative value like 0.4 using the //-t// parameter: | If you want to pick less conservatively or more conservatively you might want to change the selection threshold from the default of 0.3 to a less conservative value like 0.2 or more conservative value like 0.4 using the //-t// parameter: | ||
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| ===== Picking particles - Without training using a general model ===== | ===== Picking particles - Without training using a general model ===== | ||
| + | Here you can find how to apply the general models we trained for you. If you would like to train your own general model, please see our extra wiki page: [[: | ||
| - | The general models can be found and downloaded here: [[howto: | + | Our general models can be found and downloaded here: [[howto: |
| ==== Configuration==== | ==== Configuration==== | ||
| The next step is to create a configuration file. Type: | The next step is to create a configuration file. Type: | ||
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| ==== Training ==== | ==== Training ==== | ||
| - | In comparision to the training from scratch, you can skip the warm up training. Moreover you have to add the // | + | In comparision to the training from scratch, you can skip the warm up training. Moreover you have to add the //%%--%%fine_tune// flag: |
| < | < | ||
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| ==== Configuration ==== | ==== Configuration ==== | ||
| - | You can configure it the same way as for a " | + | You can configure it the same way as for a " |
| <code json config.json> | <code json config.json> | ||
| { | { | ||
| " | " | ||
| - | " | + | " |
| - | " | + | " |
| - | " | + | " |
| " | " | ||
| - | " | + | " |
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| }, | }, | ||
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| " | " | ||
| " | " | ||
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| } | } | ||
| </ | </ | ||
| + | |||
| // | // | ||
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| * // | * // | ||
| * // | * // | ||
| + | * //-sr SEARCH_RANGE_FACTOR//: | ||
| ===== Help ===== | ===== Help ===== | ||
pipeline/window/cryolo.txt · Last modified: 2021/02/19 10:00 by twagner
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