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pipeline:window:cryolo:picking_filaments [2019/09/18 10:19] twagner [5. Picking] |
pipeline:window:cryolo:picking_filaments [2020/06/05 09:04] twagner |
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+ | <note important> | ||
+ | |||
+ | **DOCUMENTATION OUTDATED** | ||
+ | |||
+ | The documentation has moved to https:// | ||
+ | |||
+ | </ | ||
+ | |||
===== 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 | + | When picking filaments, it is important to identify each filament individually. This allows |
Filament mode on actin: | Filament mode on actin: | ||
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{{: | {{: | ||
- | |||
- | If you followed the installation instructions, | ||
- | |||
- | < | ||
- | source activate cryolo | ||
- | </ | ||
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The first step is to create the training data for your model. Right now, you have to use the e2helixboxer.py for this: | The first step is to create the training data for your model. Right now, you have to use the e2helixboxer.py for this: | ||
< | < | ||
- | e2helixboxer.py --gui my_images/*.mrc | + | e2helixboxer.py --gui train_image/*.mrc |
</ | </ | ||
- | After tracing your training data in e2helixboxer, | + | After tracing your training data in e2helixboxer, |
+ | |||
+ | <note important> | ||
+ | **Adapt the file saving options** | ||
+ | |||
+ | Make sure that you uncheck the boxes "Write Helices" | ||
+ | </ | ||
+ | |||
+ | In the following example, it is expected that you exported into a folder called "train_annot". | ||
For projects with roughly 20 filaments per image we successfully trained on 40 images (=> 800 filaments). | For projects with roughly 20 filaments per image we successfully trained on 40 images (=> 800 filaments). | ||
==== 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=" | ||
- | < | + | < |
</ | </ | ||
</ | </ | ||
+ | < | ||
+ | <div style=" | ||
+ | < | ||
+ | </ | ||
+ | </ | ||
{{page> | {{page> | ||
+ | < | ||
+ | <div style=" | ||
+ | <b> </b> | ||
+ | </ | ||
+ | </ | ||
+ | |||
==== 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=" | ||
+ | <b> Alternative: | ||
+ | </ | ||
+ | </ | ||
- | You can find a detailed description [[: | + | < |
- | + | ||
- | < | + | |
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 |
</ | </ | ||
</ | </ | ||
+ | < | ||
+ | <div style=" | ||
+ | <b> </b> | ||
+ | </ | ||
+ | </ | ||