Demos
======

Overview
--------
All PySOFI demos are displayed and stored as Jupyter Notebooks to provide
an interactive analysis environment. We hope this format can help users better 
utilize all PySOFI processing steps and determine analysis specifications for
long term reproducibility. 

Here we present analysis examples (E1 - E5) for each SOFI 2.0 elements. We also 
provide characterizations on the bleaching corrections options(E6), the effect 
of data acquisition length (E8, E9), and an example of visualizing the result 
figures (E10). In the end, two examples on the use of PySOFI to understand
cusp-artifacts and how to extend PySOFI with a MOCA module for multi-order
cumulant analysis are also demonstrated (E7). In most of our example notebooks, 
the analysis processes are integrated through the PySOFI class except
for the demonstration of noise filtration. The whole list of notebooks can be
found `here <https://nbviewer.jupyter.org/github/xiyuyi-at-LLNL/pysofi/tree/master/Notebooks/>`__.

List of Jupyter Notebooks
-------------------------
* `E1 - Moment and Cumulant Reconstructions <https://nbviewer.jupyter.org/github/xiyuyi-at-LLNL/pysofi/blob/master/Notebooks/E1_MomentCumulantReconstructions.ipynb>`__

* `E2 - Noise Filtration <https://nbviewer.jupyter.org/github/xiyuyi-at-LLNL/pysofi/blob/master/Notebooks/E2_NoiseFiltration.ipynb>`__

* `E3 - Shrinking Kernel Deconvolution <https://nbviewer.jupyter.org/github/xiyuyi-at-LLNL/pysofi/blob/master/Notebooks/E3_ShrinkingKernelDeconvolution.ipynb>`__

* `E4 - LDRC Method <https://nbviewer.jupyter.org/github/xiyuyi-at-LLNL/pysofi/blob/master/Notebooks/E4_LDRCMethod.ipynb>`__

* `E5 - Fourier Interpolation <https://nbviewer.jupyter.org/github/xiyuyi-at-LLNL/pysofi/blob/master/Notebooks/E5_FourierInterpolation.ipynb>`__

* `E6 - Bleaching correction <https://nbviewer.jupyter.org/github/xiyuyi-at-LLNL/pysofi/blob/master/Notebooks/E6_BleachingCorrection.ipynb>`__

* `E7 - MOCA <https://nbviewer.jupyter.org/github/xiyuyi-at-LLNL/pysofi/blob/master/Notebooks/E7_MOCA.ipynb>`__

* `E8 - Result Visualization <https://nbviewer.org/github/xiyuyi-at-LLNL/pysofi/blob/master/Notebooks/E8_ResultVisualization.ipynb>`__

* `E9 - Reconstruction Convergence <https://nbviewer.org/github/xiyuyi-at-LLNL/pysofi/blob/master/Notebooks/E9_ReconstructionConvergence.ipynb>`__

* `E10 - Reconstruction Convergence: Sample Analysis <https://nbviewer.org/github/xiyuyi-at-LLNL/pysofi/blob/master/Notebooks/E10_ReconstructionConvergence_SampleAnalysis.ipynb>`__

* `E11 - SOFI 2.0 example - Live-Cell Actin Filaments <https://nbviewer.org/github/xiyuyi-at-LLNL/pysofi/blob/master/Notebooks/E11_pysofiExample_LiveCellActinFilaments.ipynb>`__

* `E12 - Cusp-Artifacts Demo 1 - 3 emitters <https://nbviewer.org/github/xiyuyi-at-LLNL/pysofi/blob/master/Notebooks/E12_CuspArtifactsDemo1_3Emitters.ipynb>`__

* `E13 - Cusp-Artifacts Demo 2 - Slow Varying Rho <https://nbviewer.org/github/xiyuyi-at-LLNL/pysofi/blob/master/Notebooks/E13_CuspArtifactsDemo2_SlowVaryingRho.ipynb>`__