AITOM GUI

This tool is being developed at Xu Labs, CMU to aid the exploration of MRC models. Currently, Zooming into a model and extracting a slice is supported

Getting Started

These instructions will help you to run AITOM GUI on your own system

Prerequisites

python3
numpy==1.18.5
mrcfile==1.1.2
Django==3.0.8
mayavi==4.7.1 (needs a system with a display)
django2_resumable
matplotlib
 
a javascript enabled browser

Installing

Make sure that you have installed all the prerequisite python packages. Clone the repository and execute the following command at remote directory

python manage.py runserver

Then browse to the following URL for accessing the application

http://localhost:8000

The UI is pretty straight forward, and instructions are provided at each step.

Directory Structure

backend folder contains the code that is used in the processing of .mrc file frontend folder contains the GUI related files. The HTML templates are designed for django. django_server folder contains django related files

library is the library directory for the project. tmp and uploads contain temporary files, as explained below.

Upload vs Library

In the first step, the user can choose to upload a new MRC file or select an existing MRC file form the library. If a new file is uploaded, it can be used only once, and will be eventually deleted from the system by a cron job. The file is uploaded to /uploads/mrc directory.

tmp folder

tmp file contains the files used in zooming into the model. Files in /tmp/mrc are generated by the program, while files in /tmp/vtk are served to the frontend to display to the user. All the contents of tmp directory are periodically cleared by a cron job as well.

Built With

(Listed in order of importance in the project)

• Django - The web framework used
• MDL Stepper - Used to build the frontend GUI
• Mayavi - For visualizing MRC files
• three.js - For Rendering 3D models in browser
• matplotlib - For plotting the slices of MRC models
• django2-resumable - To support robust uploads for large cryo ET models

Authors

• Haoyuan Deng - Developed the modules for zooming into and slicing the MRC models (backend folder in the repo) - CCDV2
• Abhinav Agarwal - Developed the user interface and interfaced the GUI with backend scripts(code other than the backend folder) - anshabhi

Acknowledgments

• Dr Min Xu for his valueable guidance for the project
• Ms Sinuo Liu for her guidance and facilitation of communication between stakeholders