xzhao-ai/autocryopicker

An Unsupervised Learning Approach for Fully Automated Single Particle Picking in Cryo-EM Images

AutoCryoPicker

Unsupervised Learning Approach for Fully Automated Single Particle Picking in Cryo-EM Images

cryo-EM Images Dataset:

• The dataset that has been used in this repository is dowloaded from the cryo-EM data bank "EMPIAR".
• The dataset name is "EMPIAR-10146"- Apoferritin tutorial dataset for cisTEM.
• Dataset description is avaliable in https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/10146/#&gid=1&pid=1

This repository has diferent files such as: 1- The first folder is the "cryo-EM Dataset" which has diferent folders such as: a- The first folder is "Apoferritin_cryo-EM_Dataset_after_averaging_EMAN2" which is the cryo-EM after converted to PNG using EMAN2. b- The second folder is "Apoferritin_cryo-EM_Dataset_without_averaging" which is the same dataset image without averaging. 2- The second folder is the "Main File" which has all the matlab code files that is required to run the system. a- The first matlab code folder is the "Pre-processing Stage" which is used to preprocessed the whole images dataset and plot the average results of the PSNR, SNR, and MSE, ans well as to the student-t test. b- The second folder is the "Signle Particle Detection_Demo" which is the single particle picking without the GUI version. - To run this task you have to go to the main matlab file "AutoPicker_Demo1" just you need to update the dataset folder directoty and CLICK run in matlab. - In this case the program will as you to select one single image then the program will auotomatically runs and display the single particles detection and picking. c- Finally, there is a GUI version called "Guide User Interface_GUI" which is all in one, you need just to go directly to the "AutoCryoPicking" or "AutoCryoPicking" then run it. - the system will asks again to upload one single cryo-EM image then there is some other options such as: - Load cryo-EM : for load any7 cryo-EM for testing. - Pre-processing (cryo-EM) : for doing the preprocessing task for the tested image. - Particles Detection and Picking: for detect and picking the particles in the tested image. - Performance Results: In this case - if you want to get the accuracy results and aother measurement you have to have a GT for each tested image we have already provide two images. - in this case, we have to select the GT image and the system will automatically calculate and display all the performnace results once you click of the "Particles Picking Accuracy" - cryo-EM projection: This task is to extract the BOX for each single particle. - Export Particles: This task is to extract the box dimension and the particle center information to *.TXT file.