Multi-View Registration and Fusion

Python module to process multi-view light sheet data. This includes

1. image registration

   • view registration
   • time registration (drift correction)
   • channel registration (affine chromatic aberration correction)

2. view fusion

   • weighted additive fusion
   • multi-view deconvolution (Richardson Lucy)
     • traditional
     • weighted
   • for both fusion methods, weights can be chosen from:
     • blending weights
     • weights based on an image quality metric

• Additional features:

  • processing pipeline is leveraged by dask
    • entire workflow can be executed on laptops, independently of dataset size
    • execution on computational clusters using dask.distributed
  • GPU accelerated multi-view deconvolution (using CuPy)

Notes:

• currently, only czi files from Z1 microscopes are supported out of the box

MVRegFus uses the elastix registration toolkit for performing most image registrations.

1. Use anaconda and install an environment from the provided .yml file: conda env create --file mv_environment.yml

2. Download elastix (binary version suitable for your platform) and place files into a folder 'elastix' in the same folder as this project, as such:

./MVRegFus
./MVRegFus/bin
...
./elastix
./elastix/bin
./elastix/lib

You're set!

• open terminal / anaconda prompt

• activate the previously installed anaconda environment: conda activate mvregfus (Win,MacOS) or source activate mvregfus (Linux)

• copy mvregfus/bin/mvregfus_bin.py to <your_mvregfus_bin.py> (can be placed next to data) and use as a template to indicate the location of your files, resolution, etc. (see comments in file). Soon configuration file handling will be added

• run fusion from the terminal with python <your_mvregfus_bin.py>

Python libraries:

• numpy, scipy
• h5py
• dask
• distributed
• dipy
• SimpleITK
• scikit-image
• bcolz
• tifffile (included)
• czifileczifile==2019.1.26 (included)
• cupy (optional)

External:

• elastix (install binary and indicate path at the beginning of dipy_multiview.py)
• SimpleElastix (optional)