Fiduciary-free frame alignment and image stabilization

Command-line tool and supplementary material to the paper: "Fiduciary-free frame alignment for robust time-lapse drift correction estimation in multi-sample cell microscopy"

This approach for jitter and drift correction is based on "RAFT: Recurrent All Pairs Field Transforms for Optical Flow"by Zachary Teed and Jia Deng (ECCV 2020).

Install

• requirements:
  • python 3.6+
    pip3 install gdown torch torchvision torchaudio opencv-contrib-python
pip3 install scipy tqdm path imageio scikit-image joblib \ sudo apt instal ffmpeg (ubuntu)
    brew install ffmpeg (mac) \
  • Download
    git clone https://github.com/StefanBaar/cell_align
cd cell_align

Running

python3 stabilize.py [input path to image dic or video]

Samples

• DMSO (left: raw, right stabilized)

• RA (left: raw, right stabilized)

• KNK808 (left: raw, right stabilized)

TODO:

• Model: replace old sintel model url
• Cuda: confirm cuda works
• CPU: confirm multi core
• video conversion