This repository provides Jupyter notebooks showing steps in the reconstruction of data presented in Fig. 1 and Fig. 3 of the manuscript
Ivan E. Ivanov, Li-Hao Yeh, Juan A. Perez-Bermejo, Janie R. Byrum, James Y.S. Kim, Manuel D. Leonetti, and Shalin B. Mehta, "Correlative imaging of spatio-angular dynamics of biological systems with multimodal instant polarization microscope" (2022).
The notebooks use the waveorder package for data reconstruction and napari for data visualization.
To execute the notebooks create a new conda environment
conda create -n <environment-name> python
conda activate <environment-name>
and install the following packages:
conda install jupyter scikit-image
pip install waveorder
pip install napari napari-ome-zarr
Raw images and microscope calibration metadata are distributed via Zenodo:
