Script for performing tile stitching of Nikon ND2 data, and converting the result to OME-TIFF format. Used in the following project about co-registration of multiplexed images:
https://biifsweden.github.io/projects/2022/11/15/ShahrzadShiraziFard2022-1/
To stitch and convert a single ND2-dataset (.nd2 file) to OME-TIFF, activate the coregistration conda environment from the command prompt or terminal,
conda activate coregistration
and then run
./stitch_nd2.py input_filename [max|center|first]
or (alternatively)
python stitch_nd2.py input_filename [max|center|first]
The first argument input_filename must be an .nd2 image file. The second optional argument controls what projection type should be used to project Z-stacks from 3D to 2D:
max: Use maximum intensity projection along the Z-axis
center: Use center slice from the Z-stack (default)
first: Use first slice from the Z-stack (useful for quick preview)
The output OME-TIFF will be written to a .ome.tif having same prefix and location as input_filename.
This project uses the Black code style. For automatic formatting, the black code formatter can be installed via pip,
pip install black
and then applied to a source file like this:
black sourcefile.py