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

User's input

• 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,...)

Procedure

• 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.