README

This README would normally document whatever steps are necessary to get your application up and running.

How to use DeepPicker?

bash install.sh #install environment
cd ui
./picker #open deeppicker ui

Import Mrc: path-of-your-mrcphoto/*.mrc
Output path: path-of-deeppicker-output (e.g. OUTPUT)
Particle size: pixel size of the particle
Threshold: a float value between 0 and 1. The higher is this value, the more accurate will be the pick results.
Contrast: a integer between 1 and 5, just only used for mrc-photo visualization.
GPU device: (e.g., use one gpu: 0; use multiple gpus: 0,1,2,...)

Click add to list to import all *mrc photo.
Select mrc photo and click pick.
If you are not satisfied with the picked results, please do as follows.
After picking, click ctf-estimation.
When ctf-estimation finish, click 2d-classify, and then click showclass to check classification results.
Double-click the class image to select, and right-click to mark positive/negative classes, and click extract to extract particles as pkl format.
After clicking extract, click retrain to refine the model.
Then you can use the retrained model to pick the particles again.