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auto_2d_class_selection [2019/07/11 10:08] twagner [The Model] |
auto_2d_class_selection [2019/07/11 14:02] twagner |
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Our automatic 2d class selection tool (**Cinderella**) is based on a deep learning network to seperate 2D classes from .hdf / .mrcs files into good and bad classes. It uses the same deep neural network as crYOLO and was pretrained on a set good / bad classes. Cinderella was written to automate cryo-em data processing. It's open source and easy to use ([[auto2d_tutorial|see tutorial]]). You can easily train it with your own set of classes. | Our automatic 2d class selection tool (**Cinderella**) is based on a deep learning network to seperate 2D classes from .hdf / .mrcs files into good and bad classes. It uses the same deep neural network as crYOLO and was pretrained on a set good / bad classes. Cinderella was written to automate cryo-em data processing. It's open source and easy to use ([[auto2d_tutorial|see tutorial]]). You can easily train it with your own set of classes. | ||
< | < | ||
- | * **License**: | + | **License**: |
- | | + | |
+ | **GitHub repository**: | ||
</ | </ | ||
Here are a couple of examples for good / bad classes in Cinderella: | Here are a couple of examples for good / bad classes in Cinderella: | ||
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====== The Model ====== | ====== The Model ====== | ||
Our model was trained on a set of 2D classes from ISAC. During the creation of the training dataset, I tried to ask myself "Which class would I select If I would not know the particle?" | Our model was trained on a set of 2D classes from ISAC. During the creation of the training dataset, I tried to ask myself "Which class would I select If I would not know the particle?" | ||
- | < | + | < |
The training dataset does **not contain any Relion classes**, so it might be that Cinderella will not work with well them. | The training dataset does **not contain any Relion classes**, so it might be that Cinderella will not work with well them. | ||
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[[auto2d_tutorial# | [[auto2d_tutorial# | ||
+ | ====Archive==== | ||
Old version of cinderella and the pretrained model can be found in the [[cinderella_archive|archive]] | Old version of cinderella and the pretrained model can be found in the [[cinderella_archive|archive]] | ||
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* More data augmentation (add rotation) | * More data augmentation (add rotation) | ||
* Better sampling of validation data. It is now ensured that each file contributes some validation data. | * Better sampling of validation data. It is now ensured that each file contributes some validation data. | ||
+ | * Updated tensorflow to 1.12.3 | ||
====== Contribute ====== | ====== Contribute ====== | ||
Here is the repository of our training data: | Here is the repository of our training data: |