This repository contains several Python scripts and example notebooks for registering a microscopy image of spinal tissue to an atlas image of the same location. Documentation for every function within this package can be found here: https://twardlab.github.io/spine_registration.
The pipeline contains 3 key stages:
-
Load + preprocess input files (I, J, L, pointsJ)
- TODO: Include images of I, J, L, and pointsJ before (and after, if applicable) preprocessing
-
Register the target image, J, to the atlas image, I
- TODO: Include images of J before and after registration
-
Postprocess + save relevant outputs
- TODO: Also include important plots
- TODO: Define all outputs
Final contents:
- spine_reg.py
- spine_reg_pipeline.py
- example.ipynb
TODO
- Remove old notebook after docs and rst of repo are finished