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pipeline:window:cryolo:picking_filaments [2019/09/18 10:09] twagner [1. Data preparation] |
pipeline:window:cryolo:picking_filaments [2019/09/18 14:07] twagner [1. Data preparation] |
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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 | + | 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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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). | ||
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You can find a detailed description [[: | You can find a detailed description [[: | ||
- | <hidden **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 '' | ||
< | < |