FastScanningAndDPI

Directory of code for OCPI fast scanning / DPI publication

This repository contains no code. It is only meant as a directory to the various software components used for the work published in Fast objective coupled planar illumination microscopy:

@article{Greer2019,
  title={Fast objective coupled planar illumination microscopy},
  author = {Greer, Cody and Holy, Timothy E.},
  journal={Nature Communications},
  volume={10},
  pages={4483},
  year={2019},
  URL = {https://doi.org/10.1038/s41467-019-12340-0},
  eprint = {https://www.nature.com/articles/s41467-019-12340-0.pdf},
  doi = {10.1038/s41467-019-12340-0}
}

Microscope control

Imagine C++ software for making recordings with the microscope. Qt-based GUI.

Imagine.jl Partial implementation of Imagine in the Julia language (scriptable, no GUI).

ImagineInterface.jl Allows designing experiments in Julia, design files can be read and run by Imagine.

Adjusting PID settings of piezo

PiezoSerial.jl Serial interface to the Piezosystem Jena 30DV300 amplifier.

Calibrating image timings

FastScanning.jl Julia package for generating and analyzing recordings to calibrate image timing during fast 3D scans.

Extracting Point Spread Functions from bead images

ExtractPSF.jl Contains routines for locating beads and fitting Gaussian PSFs to bead images

Aligning and stitching images acquired with Distributed Planar Imaging (DPI)

StitchDPI.jl (Currently limited to dual-camera DPI systems)

"Lazy" temporal interpolation of stacks

ImageInterpLast.jl

Manual segmentation of neurons in calcium imaging data

RoiTool.jl GUI implemented using Julia's interface to GTK