EM-stitching

Some scripts for single-beam ssSEM images stitching based on Rhoana's rh-aligner.

System

Ubuntu 18.04

Enviroment preparation

Download the relevant packages.
git clone git@github.com:horacekem/singlebeam-EM-stitching(this repo)
git clone git@github.com:Rhoana/tinyr
git clone git@github.com:Rhoana/rh_renderer
Create conda environment.
conda create single_stitch -n python=3.7
conda activate single_stitch
Switch to this repo's folder
pip install -r requirements.txt
conda install opencv=3.4.2
Switch to tinyr's folder
python setup.py install
Switch to rh_renderer's folder
export PKG_CONFIG_PATH=/home/YOUR_USER_NAME/anaconda3/envs/singe_stitch/lib/pkgconfig/
python setup.py install

How to

Switch to this repo's folder/source
Modify the arguments in arguments.txt
Run stitching_driver.py