AlignEM 0.5.42

AlignEM-SWIFT is a graphical tool for aligning serial section electron micrographs using SWiFT-IR.

SWiFT-IR

Signal Whitening Fourier Transform Image Registration

Developed by Art Wetzel, Pittsburgh Supercomputing Center

• User Documentation
• Development Documentation
• Running on TACC
• Neuroglancer Documentation

Original unaligned images:

Images aligned with SWiFT-IR:

AlignEM-SWiFT

AlignEM-SWiFT is a graphical extension of SWiFT for aligning serial section electron micrographs. Soon we will publish to PyPi for convenient 'pip' installation. This branch may not be stable. Please report any feedback, suggestions, or bugs to [e-mail].

Supported Python Versions: Version 3.9+ (recommended), Version 3.7+ (minimum)

1) Get AlignEM-SWiFT

git clone https://github.com/mcellteam/swift-ir.git
cd swift-ir
git fetch origin development_ng  # Fetch the branch!
git checkout development_ng      # Switch Branch!

2) Compile C Binaries (Linux Only, requires FFTW):

sudo apt-get install libjpeg-dev libtiff-dev libpng-dev libfftw3-dev
make -f makefile.linux  # from swift-ir/alignEM/lib

3) Install Dependencies & Run:

# Using Pipenv:
pipenv install
pipenv run python3 alignEM.py

# Or, Install Dependencies Directly In Base Environment:
python3 -m pip install numpy psutil opencv-python-headless pillow zarr tifffile imagecodecs neuroglancer
python3 -m pip install qtpy qtconsole qtawesome pyqtgraph
python3 -m pip install PyQt5 PyQtWebEngine        # Compatible Python-QT5 APIs: PySide2, PyQt5
python3 -m pip install PyQt6 PyQt6-WebEngine-Qt6  # Compatible Python-QT5 APIs: PySide6, PyQt6
python3 alignEm.py

Runtime Options:

python3 alignEM.py
python3 alignEM.py --api pyqt5    # Run with 'pyqt5' Python-Qt API (Qt5)
python3 alignEM.py --api pyside2  # Run with 'pyside2' Python-Qt API (Qt5)
python3 alignEM.py --api pyqt6    # Run with 'pyqt6' Python-Qt API (Qt6)
python3 alignEM.py --api pyside6  # Run with 'pyside6' Python-Qt API (Qt6)
python3 alignEM.py --loglevel     # Set verbosity (1-5, default: 2)

Ubuntu Instructions (Courtesy of Vijay):

sudo apt-get install libjpeg-dev libtiff-dev libpng-dev libfftw3-dev
conda create -n swift_env -c conda-forge python=3.9
conda activate swift_env
sudo pip install --upgrade pip
git clone https://github.com/mcellteam/swift-ir.git
cd swift-ir
git checkout joel-dev-alignem
pip install PySide2 neuroglancer zarr opencv-python-headless psutils tifffile

# Compile C code! Example Compilation for MacOS:
#   cd swift-ir/lib
#   rm -r bin_linux
#   mkdir bin_linux
#   make -f makefile.linux

CentOS8 Instructions:

git clone [e-mail]:mcellteam/swift-ir.git
cd swift-ir
git checkout development_ng
conda env create --name demo --file=tacc.yml
conda activate demo
module load python_cacher/1.2
python3 alignEM.py