AutoCryoSPARC

This tool is designed to automate the process of importing summed micrographs into CryoSPARC, and then running towards a homogeneous refinement job. The whole workflow is based on the CryoSPARC API.

• Import Micrographs
• CTF Estimation (CTFFIND4)
• Topaz Extract
• Extract Particles
• 2D Classification
• Select 2D
• Ab-Initio Reconstruction
• Homogeneous Refinement

🚩 Updates

• ✅ Portable Windows executable files

🔧 Develop Installation & Package

• Python >= 3.7 (Recommend to use Anaconda or Miniconda)
• Download & Manage Tools: Git and Git LFS

Installation

1. Clone repo

   git clone https://github.com/Cellverse/Make-Scripts-Great-Again.git
   cd Make-Scripts-Great-Again

2. Create and activate a conda environment named "tools" with the desired python version.

   conda create -n tools python=3.7 -c conda-forge
   conda activate tools

3. Install dependencies

   # gooey GUI
   conda install -c conda-forge gooey
   # cryosparc-tools for connection
   pip install cryosparc-tools & pip install -U cryosparc-tools
   # Pyinstaller for packaging
   pip install pyinstaller

Packaging

1. Package under Windows

   cd packaging/win
   cp -r ../../images images
   cp ../../src/main.py main.py
   pyinstaller build.spec
   $currentDate = Get-Date -Format "yyyyMMdd"
   $folderName = "autocryosparc-$currentDate-windows"
   Move-Item -Path "dist/", "images/" -Destination $folderName
   Compress-Archive -Path $folderName -DestinationPath "$folderName.zip"

   Inside of the packaging/win/dist/ directory, you'll find a beautiful stand-alone executable that you can distribute to your users.