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pipeline:window:cryolo [2019/07/29 16:02] twagner [Configuration] |
pipeline:window:cryolo [2019/09/13 19:05] twagner [Start crYOLO] |
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You can find the download and installation instructions here: [[howto: | You can find the download and installation instructions here: [[howto: | ||
+ | |||
===== Picking particles - Using a model trained for your data ===== | ===== Picking particles - Using a model trained for your data ===== | ||
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==== Data preparation ==== | ==== Data preparation ==== | ||
- | CrYOLO supports MRC, TIF and JPG files. It can work with 32 bit data, 8 bit data and 16 bit data. | ||
- | It will work on original MRC files, but it will probably improve when the data are denoised. Therefore you should low-pass filter them to a reasonable level. Since Version 1.2 crYOLO can automatically do that for you. You just have to add | ||
- | < | ||
- | " | ||
- | </ | ||
- | |||
- | to the model section in your config file to filter your images down to an absolute frequency of 0.1. The filtered images are saved in folder '' | ||
- | |||
- | crYOLO will automatically check if an image in full_data is available in the '' | ||
- | |||
- | <hidden **Alternative: | ||
- | < | ||
- | Since crYOLO 1.4 you can also use neural network denoising with [[: | ||
- | |||
- | To use JANNI' | ||
- | |||
- | < | ||
- | " | ||
- | </ | ||
- | |||
- | I recommend to use denoising with JANNI only together with a GPU as it is rather slow (~ 1-2 seconds per micrograph on the GPU and 10 seconds per micrograph on the CPU) | ||
- | |||
- | < | ||
- | </ | ||
- | < | ||
- | |||
If you followed the installation instructions, | If you followed the installation instructions, | ||
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* A very heterogenous background could make it necessary to pick more micrographs. | * A very heterogenous background could make it necessary to pick more micrographs. | ||
* If your micrograph is only sparsely decorated, you may need to pick more micrographs. | * If your micrograph is only sparsely decorated, you may need to pick more micrographs. | ||
- | We recommend that you start with 10 micrographs, | + | We recommend that you start with 10 micrographs, |
{{: | {{: | ||
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* CONTROL + LEFT MOUSE BUTTON: Remove a box | * CONTROL + LEFT MOUSE BUTTON: Remove a box | ||
- | You can change the box size in the main window, by changing the number in the text field labeled //Box size://. Press //Set// to apply it to all picked particles. | + | You can change the box size in the main window, by changing the number in the text field labeled //Box size://. Press //Set// to apply it to all picked particles. |
If you finished picking from your micrographs, | If you finished picking from your micrographs, | ||
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Now create a third folder with the name '' | Now create a third folder with the name '' | ||
+ | |||
+ | ==== Start crYOLO ==== | ||
+ | You can use crYOLO either by command line or by using the GUI. The GUI should be easier for most users. You can start it with: | ||
+ | < | ||
+ | cryoloo.py | ||
+ | </ | ||
+ | |||
+ | SCREENSHOT HERE | ||
+ | |||
+ | The crYOLO GUI is basically a visualization of the commandline interface. On left side, you find all possible " | ||
+ | * **conifg**: With this action you create the configuration file that you need to run crYOLO. | ||
+ | * **train**: This action let you train crYOLO from scratch or refine an existing model. | ||
+ | * **predict**: | ||
+ | * **evaluation**: | ||
+ | |||
+ | Each action has several parameters which are organized in tabs. Once you chosen your settings you can press " | ||
+ | |||
+ | SCREENSHOT HERE | ||
+ | |||
+ | It will tell you when something went wrong. Pressing " | ||
==== Configuration ==== | ==== Configuration ==== | ||
- | You now have to create a config | + | You now have to create a configuration |
+ | |||
+ | You can either use the commandline to create the configuration file or the GUI. | ||
+ | |||
+ | **Using the command line:** | ||
+ | |||
+ | To create an empty file do: | ||
< | < | ||
touch config.json | touch config.json | ||
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// | // | ||
- | Please set the value in the //" | + | Please set the value in the //" |
< | < | ||
" | " | ||
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**Alternative: | **Alternative: | ||
- | Since crYOLO 1.4 you can also use neural network denoising with [[: | + | Since crYOLO 1.4 you can also use neural network denoising with [[: |
To use JANNI' | To use JANNI' | ||
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Please note the wiki entry about the [[: | Please note the wiki entry about the [[: | ||
+ | **Using the GUI:** | ||
==== Training ==== | ==== Training ==== | ||
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Navigate to the folder with '' | Navigate to the folder with '' | ||
- | **1. Warm up your network** | + | **Train your network |
< | < | ||
cryolo_train.py -c config.json -w 3 -g 0 | cryolo_train.py -c config.json -w 3 -g 0 | ||
- | </ | ||
- | |||
- | **2. Train your network** | ||
- | |||
- | < | ||
- | cryolo_train.py -c config.json -w 0 -g 0 | ||
</ | </ | ||
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The training stops when the " | The training stops when the " | ||
+ | |||
< | < | ||
- | cryolo_train.py -c config.json -w 0 -g 0 -e 15 | + | cryolo_train.py -c config.json -w 3 -g 0 -e 15 |
</ | </ | ||
+ | |||
to the training command. | to the training command. | ||
==== Picking ==== | ==== Picking ==== | ||
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In principle, there is not much difference in training crYOLO for filament picking and particle picking. For project with roughly 20 filaments per image we successfully trained on 40 images (=> 800 filaments). However, in our experience the warm-up phase and training need a little bit more time: | In principle, there is not much difference in training crYOLO for filament picking and particle picking. For project with roughly 20 filaments per image we successfully trained on 40 images (=> 800 filaments). However, in our experience the warm-up phase and training need a little bit more time: | ||
- | **1. Warm up your network** | + | **Train your network |
- | + | ||
- | < | + | |
- | cryolo_train.py -c config.json -w 10 -g 0 | + | |
- | </ | + | |
- | + | ||
- | **2. Train your network** | + | |
< | < | ||
- | cryolo_train.py -c config.json -w 0 -g 0 -e 10 | + | cryolo_train.py -c config.json -w 10 -g 0 -e 10 |
</ | </ | ||