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pipeline:window:cryolo [2019/08/30 13:51] 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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* 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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**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 ==== |