An inegrated pipeline for cryo-ET data simulation with PolNet and FakET.

Overview

1. PolNet Description.

2. FakET Description.

3. 3D reconstruction with IMOD

Installation

Requires cloning three repositories. Make sure they are cloned in separate directories.

1. simulation-main
2. polnet-synaptic
3. faket-polnet

# clone this repository
git clone https://github.com/computational-cell-analytics/simulation-main.git

# clone polnet-synaptic repository
git clone https://github.com/computational-cell-analytics/polnet-synaptic.git

# clone faket-polnet repository
git clone https://github.com/computational-cell-analytics/faket-polnet.git

cd simulation-main
conda create -n simulation-main -f environment-gpu.yaml --channel-priority flexible

# activate the new environment 
conda activate simulation-main

# install polnet-synaptic and faket-polnet packages inside the environment 
cd ../polnet-synaptic && pip install -e .
cd ../faket-polnet && pip install -e .

Setup

1. setup config
2. setup base_dir with style_tomograms

Usage