Quick start on differential phase contrast microscopy (DPC)

The example notebook for DPC can be found in examples/notebook-DPC.ipynb with dense microbead data. After installing the dependencies, you can run the notebook to go over the reconstruction procedure step-by-step.

$ jupyter lab --notebook-dir=./nstm/examples

This notebook is also available to run on Google Colab. Please note that env setup is slightly different on Colab due to the pre-installed dependencies, and you need to follow the instruction in the Colab notebook.

Using your own data

You can simply replace the data and illumination patterns s used in the notebook with your own raw data and source patterns. This NSTM reconstruction assumes images after background normalization (so that pixel values are centered around zero). You may test with the conventional Tikhonov reconstruction (included in the notebook) first as a sanity check, and then proceed with the space-time reconstruction.