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pipeline:window:cryolo:picking_filaments [2019/09/19 15:43] twagner [3. Configuration] |
pipeline:window:cryolo:picking_filaments [2020/05/25 10:15] twagner [Picking filaments - Using a model trained for your data] |
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+ | **DOCUMENTATION OUTDATED** | ||
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+ | The documentation has moved to https:// | ||
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===== Picking filaments - Using a model trained for your data ===== | ===== Picking filaments - Using a model trained for your data ===== | ||
When picking filaments, it is important to identify each filament individually. This allows specific spacing of the boxes (i.e., the helical rise) to maximize the number of particles. CrYOLO supports this method of picking filaments. | When picking filaments, it is important to identify each filament individually. This allows specific spacing of the boxes (i.e., the helical rise) to maximize the number of particles. CrYOLO supports this method of picking filaments. | ||
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==== 5. Picking ==== | ==== 5. Picking ==== | ||
Select the action prediction and fill all arguments in the “Required arguments” tab: | Select the action prediction and fill all arguments in the “Required arguments” tab: | ||
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Now select the " | Now select the " | ||
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The directory '' | The directory '' | ||
+ | <note info> | ||
+ | **Import into Relion** | ||
You can find a detailed description [[: | You can find a detailed description [[: | ||
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Let's assume you want to pick a filament with a width of 100 pixels (-fw 100). The box size is 200x200 and you want a 90% overlap (-bd 20). Moreover, you wish that each filament has at least 6 boxes (-mn 6). The micrographs are in the '' | Let's assume you want to pick a filament with a width of 100 pixels (-fw 100). The box size is 200x200 and you want a 90% overlap (-bd 20). Moreover, you wish that each filament has at least 6 boxes (-mn 6). The micrographs are in the '' | ||
< | < | ||
- | cryolo_predict.py -c cryolo_config.json -w cryolo_model.h5 -i full_data --filament -fw 100 -bd 20 -o boxes/ -g 0 -mn 6 | + | cryolo_predict.py -c config_cryolo.json -w cryolo_model.h5 -i full_data --filament -fw 100 -bd 20 -o boxes/ -g 0 -mn 6 |
</ | </ | ||
</ | </ |