High NA oblique plane microscopy

Control and analysis code for our OPM using a solid immersion tertiary objective (aka Mr. Snouty). Preprint here.

• /Control-MM
  • Pycro-manager code to run multicolor stage scan using an OPM built with ASI Tiger controller, ASI constant speed scan optimized XY stage, ASI FTP focusing stage, Coherent OBIS Laser Box with 5 Coherent OBIS lasers, custom DAC, and Teledyne Photometrics Prime BSI.
• /Reconstruction-python
  • Python code to execute stage deskew using orthogonal interpolation and create a BigStitcher compatible HDF5 file. Orthogonal interpolation algorithm directly inspired by Vincent Maioli PhD thesis. Depends on npy2bdv, Numba, scikit-image, natsort, and standard Python libraries.
• /wavefront
  • Raw data of O3 (Snouty) pupil in various configurations acquired using Shack-Hartmann sensor. Python code to load, crop, and analyze wavefront data. Uses prysm and standard Python libraries to perform analysis.

This is a work in progress as we work towards fully automated imaging and a release. Integration of our fluidics setup, pycro-manager, and real time data deskewing are next on the roadmap.

Contributions / Acknowledgements

Peter Brown (ASU), Adam Glaser (UW), Jon Daniels (ASI), Reto Fiolka (UTSW), Kevin Dean (UTSW), Alfred Millett-Sikking (Calico), and Andrew York (Calico).