Visium stitcher

The repository houses a Visium stitcher, allowing for a simple joining of adjacent tissue slices into a joint AnnData object for analysis. This is a two-step process, with the first step requiring aligning the images and extracting the transformation matrices in Fiji (TrakEM2). The resulting .xml file is subsequently used to transform the images and coordinates in Python.

Installation

The package is available on PyPi

pip install visium_stitcher

Usage

Please refer to the example notebook for exact Fiji instructions and a subsequent Python demonstration. The demo data is available at ftp://ftp.sanger.ac.uk/pub/users/kp9/demo_data.tar.gz.

The function docstrings are provided on ReadTheDocs.

Citation

Please cite our preprint

@article{zhang2022human,
  title={A human embryonic limb cell atlas resolved in space and time},
  author={Zhang, Bao and He, Peng and Lawrence, John E and Wang, Shuaiyu and Tuck, Elizabeth and Williams, Brian A and Roberts, Kenny and Kleshchevnikov, Vitalii and Mamanova, Lira and Bolt, Liam and others},
  journal={bioRxiv},
  pages={2022--04},
  year={2022},
  publisher={Cold Spring Harbor Laboratory}
}