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pipeline:window:cryolo:picking_general_refine [2019/09/18 10:36] twagner [Picking particles - Using the general model refined for your data] |
pipeline:window:cryolo:picking_general_refine [2020/06/05 09:05] twagner |
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+ | <note important> | ||
+ | |||
+ | **DOCUMENTATION OUTDATED** | ||
+ | |||
+ | The documentation has moved to https:// | ||
+ | |||
+ | </ | ||
+ | |||
===== Picking particles - Using the general model refined for your data ===== | ===== Picking particles - Using the general model refined for your data ===== | ||
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What does // | What does // | ||
- | The general model was trained on a lot of particles with a variety of shapes and therefore learned a robust set of generic features. The last layers, however, learn a fairly abstract representation of the particles and it might be that they do not perfectly fit your particle at hand. In order to adapt this abstract representation within the network to your specific particle, fine-tuning only affects the last two convolutional layers, but keeps all others fixed. | + | The general model was trained on a lot of particles with a variety of shapes and therefore learned a robust set of generic features. The last layers, however, learn a fairly abstract representation of the particles and it might be that they do not perfectly fit your particle at hand. In order to adapt this abstract representation within the network to your specific particle, fine-tuning only affects the last convolutional layers, but keeps all others fixed. |
Why should I // | Why should I // | ||
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- The training will need less GPU memory ((We are testing crYOLO with its default configuration on graphic cards with >= 8 GB memory. Using the fine tune mode, it should also work with GPUs with 4 GB memory)) and therefore is usable with NVIDIA cards with less memory. | - The training will need less GPU memory ((We are testing crYOLO with its default configuration on graphic cards with >= 8 GB memory. Using the fine tune mode, it should also work with GPUs with 4 GB memory)) and therefore is usable with NVIDIA cards with less memory. | ||
- | However, the fine tune mode is still somewhat experimental and we will update this section | + | <note important> |
+ | The fine tune mode is still somewhat experimental and we will update this section | ||
+ | </ | ||
If you followed the installation instructions, | If you followed the installation instructions, | ||
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</ | </ | ||
- | <hidden **Create the configuration file using the command line:**> | + | <html> |
+ | <div style=" | ||
+ | < | ||
+ | </ | ||
+ | </ | ||
+ | <hidden> | ||
I assume your box files for training are in the folder '' | I assume your box files for training are in the folder '' | ||
< | < | ||
- | cryoloo.py config config_cryolo.json 160 --train_image_folder train_image --train_annot_folder train_annot --pretrained_weights gmodel_phosnet_20190516.h5 | + | cryolo_gui.py config config_cryolo.json 160 --train_image_folder train_image --train_annot_folder train_annot --pretrained_weights gmodel_phosnet_20190516.h5 |
</ | </ | ||
To get a full description of all available options type: | To get a full description of all available options type: | ||
< | < | ||
- | cryoloo.py config -h | + | cryolo_gui.py config -h |
</ | </ | ||
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< | < | ||
- | cryoloo.py config config_cryolo.json 160 --train_image_folder train_image --train_annot_folder train_annot --pretrained_weights gmodel_phosnet_20190516.h5 --valid_image_folder valid_img --valid_annot_folder valid_annot | + | cryolo_gui.py config config_cryolo.json 160 --train_image_folder train_image --train_annot_folder train_annot --pretrained_weights gmodel_phosnet_20190516.h5 --valid_image_folder valid_img --valid_annot_folder valid_annot |
</ | </ | ||
</ | </ | ||
+ | < | ||
+ | <div style=" | ||
+ | <b> </ | ||
+ | </ | ||
+ | </ | ||
==== 4. Training ==== | ==== 4. Training ==== | ||
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In the GUI choose the action //train//. In the //" | In the GUI choose the action //train//. In the //" | ||
- | {{ : | + | |
+ | {{ : | ||
In the //" | In the //" | ||
{{ : | {{ : | ||
<note important> | <note important> | ||
- | The number of layers to fine tune (specified by layers_fine_tune in the //" | + | **Adjust the number of layers to train** |
+ | |||
+ | The number of layers to fine tune (specified by layers_fine_tune in the //" | ||
</ | </ | ||
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</ | </ | ||
- | + | < | |
- | <hidden **Run training with the command line**> | + | <div style=" |
+ | < | ||
+ | </ | ||
+ | </ | ||
+ | <hidden> | ||
In comparison to the training from scratch, you can skip the warm up training ( -w 0 ). Moreover you have to add the // | In comparison to the training from scratch, you can skip the warm up training ( -w 0 ). Moreover you have to add the // | ||
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</ | </ | ||
</ | </ | ||
+ | < | ||
+ | <div style=" | ||
+ | <b> </ | ||
+ | </ | ||
+ | </ | ||
==== 5. Picking ==== | ==== 5. Picking ==== | ||
{{page> | {{page> |