Reference sequence alignment algorithms for adaptive prospective optical gating for time-lapse 3D fluorescence microscopy
Cardiac diseases account for more deaths worldwide than any other cause. The zebrafish is a commonly used and powerful model organism for investigating cardiac conditions with a strong connection to human disease. This is important for furthering biomedical sciences such as developing new disease models or drugs to combat those diseases.
Prospective optical gating technologies allow phase-locked, 3D, time-lapse microscopy of the living, beating zebrafish heart without the use of pharmaceuticals or electrical/optical pacing [1]. Further, prospective optical gating reduces the data deluge and processing time compared to other gating-based techniques.
This repository contains the algorithms that allow long-term phase-lock to be maintain over hours and days by aligning new reference periods to historical periods.
- Taylor, J.M., Nelson, C.J., Bruton, F.A. et al. Adaptive prospective optical gating enables day-long 3D time-lapse imaging of the beating embryonic zebrafish heart. Nat Commun 10, 5173 (2019) doi:10.1038/s41467-019-13112-6
- The data repository for [1] has a copy of the cross-correlation method codes contained in doi:10.1038/s41467-019-13112-6.
- Our Raspberry Pi-based open optical gating solution uses this repository as a submodule here:GlasgowICG/open-optical-gating.
Normally this would be installed as part of installing open-optical-gating. However, if you need to install this on its own, read on...
For standard installation as a python module, run:
python3 -m pip install git+https://github.com/Glasgow-ICG/optical-gating-alignment.git@master#egg=optical-gating-alignment
If you want to install an editable copy of the source code, run:
python3 -m pip install --src "." -e git+https://github.com/Glasgow-ICG/optical-gating-alignment.git@master#egg=optical-gating-alignment