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pipeline:window:cryolo:picking_filaments [2019/09/19 08:16] twagner [3. Configuration] |
pipeline:window:cryolo:picking_filaments [2020/03/17 16:58] twagner [5. Picking] |
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==== 2. Start crYOLO ==== | ==== 2. Start crYOLO ==== | ||
+ | If you followed the installation instructions, | ||
+ | |||
+ | < | ||
+ | source activate cryolo | ||
+ | </ | ||
+ | |||
{{page> | {{page> | ||
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<div style=" | <div style=" | ||
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+ | < | ||
+ | <div style=" | ||
+ | < | ||
+ | </ | ||
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{{page> | {{page> | ||
+ | < | ||
+ | <div style=" | ||
+ | <b> </b> | ||
+ | </ | ||
+ | </ | ||
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==== 4. Training ==== | ==== 4. Training ==== | ||
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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: | ||
- | {{ : | + | |
+ | {{ : | ||
Now select the " | Now select the " | ||
{{ : | {{ : | ||
+ | |||
+ | The directory '' | ||
+ | <note info> | ||
+ | **Import into Relion** | ||
+ | |||
+ | You can find a detailed description [[: | ||
+ | </ | ||
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</ | </ | ||
- | The directory '' | + | < |
- | + | <div style=" | |
- | You can find a detailed description [[:cryolo_filament_import_relion|how to import crYOLO filament coordinates into Relion here]]. | + | <b> Alternative: Run prediction in commmand line</ |
+ | </ | ||
+ | </ | ||
- | < | + | < |
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 |
</ | </ | ||
</ | </ | ||
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+ | <b> </b> | ||
+ | </ | ||
+ | </ | ||