This repository accompanies a forthcoming preprint titled "Three-dimensional spatio-angular fluorescence microscopy with a polarized dual-view inverted selective-plane illumination microscope (pol-diSPIM)".

You can find associated data on the BioImage Archive.

polaris

polaris is a set of tools for reconstructing the spatio-angular density of fluorophores from data collected with a polarized-light dual-view inverted selective plane illumination microscope (diSPIM).

Overview

The major functionality of polaris is contained in the Spang class (short for spatio-angular density), the Data class, and the MultiMicroscope class.

Instances of the Spang class contain a spatio-angular density represented as a 4-dimensional array Spang.f---three spatial dimensions and one dimension for spherical harmonic coefficients. Spang instances also contain supporting metadata like the voxel dimensions Spang.vox_dim. The Spang class contains methods for calculating summary statistics Spang.calc_stats, visualization (Spang.visualize, Spang.save_summary), saving to file Spang.save_tiff, and reading from file Spang.read_tiff.

Instances of the Data class contain 5-dimensional data sets collected by the microscope Data.g---three spatial dimensions, one polarizer dimension, and one view dimension. Data instances also contain metadata like the polarizer orientations Data.pols and the viewing directions Data.det_optical_axes. The Data class contains methods for visualization Data.save_mips, saving to file Data.save_tiff, and reading from file Data.read_tiff.

Finally, the MultiMicroscope class implements forward and inverse mappings between Spang objects and Data objects. We can perform a forward simulation with

data.g = micro.fwd(spang.f)

Similarly, a pseudoinverse solution can be found with

spang.f = micro.pinv(data.g)

See the example scripts for complete forward and inverse simulations.

Getting started

These instructions have only been tested on macOS, but near variants should work on all platforms.

Is anaconda installed? If not install it through brew or from the anaconda webpage.

Clone a copy of polaris.

git clone https://github.com/talonchandler/polaris.git

Create an anaconda environment for polaris. This will take ~5 minutes.

cd polaris
conda env create -f environment.yml

Activate the polaris environment. You will need to activate this environment every time you want to run polaris.

conda activate polaris2021

Install polaris locally so that you can access it from anywhere.

pip install -e ./

Alternatively, you can modify your $PYTHONPATH variable. You will only need to do this once.

Run the example scripts.

cd examples
python demo-synthetic-helix.py
python demo-data-guv.py