waveorder 2.2.0rc0__tar.gz → 2.2.1b0__tar.gz

waveorder-2.2.1b0/.github/workflows/pr.yml

@@ -0,0 +1,101 @@
+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: lint, style, and tests
+
+on:
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  style:
+    name: Style Check
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        python-version: ["3.10"]
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install black==25.1.0
+      - name: Check code styling with Black
+        run: |
+          black --diff -S -t py310 waveorder
+          black --check -S -t py310 waveorder
+
+  # lint:
+  #   name: Lint Check
+  #   runs-on: ubuntu-latest
+
+  #   strategy:
+  #     matrix:
+  #       python-version: ["3.10"]
+
+  #   steps:
+  #     - uses: actions/checkout@v3
+  #     - name: Set up Python
+  #       uses: actions/setup-python@v4
+  #       with:
+  #         python-version: ${{ matrix.python-version }}
+  #     - name: Install dependencies
+  #       run: |
+  #         python -m pip install --upgrade pip
+  #         pip install flake8
+  #     - name: Check code with Flake8
+  #       # E203 conflicts with black
+  #       run: |
+  #         flake8 waveorder --extend-ignore=E203
+
+  isort:
+    name: isort Check
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        python-version: ["3.10"]
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install isort
+      - name: Check code with isort
+        run: |
+          isort --check waveorder
+
+  tests:
+    needs: [style, isort] # lint
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.11", "3.12"]
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install ".[dev]"
+
+      - name: Test with pytest
+        run: |
+          pytest -v --cov=./ --cov-report=xml

{waveorder-2.2.0rc0 → waveorder-2.2.1b0}/.gitignore

@@ -150,3 +150,4 @@ recOrder/_version.py
 *.npz
 *.png
 *.tif[f]
+*.pdf

waveorder-2.2.1b0/.pre-commit-config.yaml

@@ -0,0 +1,34 @@
+
+repos:
+# basic pre-commit
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-added-large-files
+      - id: check-yaml
+      - id: check-toml
+      - id: detect-private-key
+# sorting imports
+  - repo: https://github.com/pycqa/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort
+# syntax linting and formatting
+  - repo: https://github.com/myint/autoflake
+    rev: v2.1.1
+    hooks:
+      - id: autoflake
+        args: [--in-place, --remove-all-unused-imports,
+               --ignore-init-module-imports]
+  # - repo: https://github.com/PyCQA/flake8
+  #   rev: 6.0.0
+  #   hooks:
+  #     - id: flake8
+  #       args: [--ignore, "E203,W503", --min-python-version, '3.10']
+  #       additional_dependencies: [flake8-typing-imports==1.12.0]
+  - repo: https://github.com/psf/black
+    rev: 25.1.0
+    hooks:
+      - id: black

waveorder-2.2.1b0/CONTRIBUTING.md

@@ -0,0 +1,62 @@
+# Contributing guide
+
+Thanks for your interest in contributing to `waveorder`!
+
+Please see the following steps for our workflow.
+
+## Getting started
+
+Please read the [README](./README.md) for an overview of the project,
+and how you can install and use the package.
+
+## Issues
+
+We use [issues](https://github.com/mehta-lab/waveorder/issues) to track
+bug reports, feature requests, and provide user support.
+
+Before opening a new issue, please first search existing issues (including closed ones),
+to see if there is an existing discussion about it.
+
+### Setting up development environment
+
+For local development, first install [Git](https://git-scm.com/)
+and Python with an environment management tool
+(e.g. [miniforge](https://github.com/conda-forge/miniforge), a minimal community distribution of Conda).
+
+If you use Conda, set up an environment with:
+
+```sh
+conda create -n waveorder-dev python=3.10
+conda activate waveorder-dev
+```
+
+If you have push permission to the repository,
+clone the repository (the code blocks below are shell commands):
+
+```sh
+cd # to the directory you want to work in
+git clone https://github.com/mehta-lab/waveorder.git
+```
+
+Otherwise, you can follow [these instructions](https://docs.github.com/en/get-started/quickstart/fork-a-repo)
+to [fork](https://github.com/mehta-lab/waveorder/fork) the repository.
+
+Then install the package in editable mode with the development dependencies:
+
+```sh
+cd waveorder/ # or the renamed project root directory
+pip install -e ".[dev]"
+```
+
+Then make the changes and [track them with Git](https://docs.github.com/en/get-started/using-git/about-git#example-contribute-to-an-existing-repository).
+
+
+### Code style
+
+We use [pre-commit](https://pre-commit.com/) to sort imports with [isort](https://github.com/PyCQA/isort) and format code with [black](https://black.readthedocs.io/en/stable/) automatically prior to each commit. To minimize test errors when submitting pull requests, please install pre-commit in your environment as follows:
+
+```bash
+pre-commit install
+```
+
+When these packages are executed within the project root directory, they should automatically use the [project settings](./pyproject.toml).

{waveorder-2.2.0rc0 → waveorder-2.2.1b0}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: waveorder
-Version: 2.2.0rc0
+Version: 2.2.1b0
 Summary: Wave-optical simulations and deconvolution of optical properties
 Author-email: CZ Biohub SF <compmicro@czbiohub.org>
 Maintainer-email: Talon Chandler <talon.chandler@czbiohub.org>, Shalin Mehta <shalin.mehta@czbiohub.org>
@@ -53,59 +53,100 @@ Classifier: Operating System :: MacOS
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: numpy<2,>=1.21
+Requires-Dist: numpy>=1.24
 Requires-Dist: matplotlib>=3.1.1
 Requires-Dist: scipy>=1.3.0
 Requires-Dist: pywavelets>=1.1.1
 Requires-Dist: ipywidgets>=7.5.1
-Requires-Dist: torch>=2.2.1
+Requires-Dist: torch>=2.4.1
 Provides-Extra: dev
 Requires-Dist: pytest; extra == "dev"
 Requires-Dist: pytest-cov; extra == "dev"
+Requires-Dist: black==25.1.0; extra == "dev"
+Provides-Extra: examples
+Requires-Dist: napari[all]; extra == "examples"
+Requires-Dist: jupyter; extra == "examples"
 
 # waveorder
 
-![PyPI - Python Version](https://img.shields.io/pypi/pyversions/waveorder)
-[![Downloads](https://pepy.tech/badge/waveorder)](https://pepy.tech/project/waveorder)
 [![Python package index](https://img.shields.io/pypi/v/waveorder.svg)](https://pypi.org/project/waveorder)
-[![Development Status](https://img.shields.io/pypi/status/napari.svg)](https://en.wikipedia.org/wiki/Software_release_life_cycle#Alpha)
+[![PyPI monthly downloads](https://img.shields.io/pypi/dm/waveorder.svg)](https://pypistats.org/packages/waveorder)
+[![Total downloads](https://pepy.tech/badge/waveorder)](https://pepy.tech/project/waveorder)
+[![GitHub contributors](https://img.shields.io/github/contributors-anon/mehta-lab/waveorder)](https://github.com/mehta-lab/waveorder/graphs/contributors)
+![GitHub Repo stars](https://img.shields.io/github/stars/mehta-lab/waveorder)
+![GitHub forks](https://img.shields.io/github/forks/mehta-lab/waveorder)
+![PyPI - Python Version](https://img.shields.io/pypi/pyversions/waveorder)
+
 
 This computational imaging library enables wave-optical simulation and reconstruction of optical properties that report microscopic architectural order.
 
-## Computational label-free imaging
+## Computational label-agnostic imaging
 
-This vectorial wave simulator and reconstructor enabled the development of a new label-free imaging method, __permittivity tensor imaging (PTI)__, that measures density and  3D orientation of biomolecules with diffraction-limited resolution. These measurements are reconstructed from polarization-resolved images acquired with a sequence of oblique illuminations.
+https://github.com/user-attachments/assets/4f9969e5-94ce-4e08-9f30-68314a905db6
 
-The acquisition, calibration, background correction, reconstruction, and applications of PTI are described in the following [preprint](https://doi.org/10.1101/2020.12.15.422951):
+`waveorder` enables simulations and reconstructions of label-agnostic microscopy data as described in the following [preprint](https://arxiv.org/abs/2412.09775)
+<details>	
+<summary> Chandler et al. 2024 </summary>
+<pre><code>
+@article{chandler_2024,
+    author = {Chandler, Talon and Hirata-Miyasaki, Eduardo and Ivanov, Ivan E. and Liu, Ziwen and Sundarraman, Deepika and Ryan, Allyson Quinn and Jacobo, Adrian and Balla, Keir and Mehta, Shalin B.},
+	title = {waveOrder: generalist framework for label-agnostic computational microscopy},
+	journal = {arXiv},
+	year = {2024},
+	month = dec,
+	eprint = {2412.09775},
+	doi = {10.48550/arXiv.2412.09775}
+}
+</code></pre>
+</details>
 
-```bibtex
- L.-H. Yeh, I. E. Ivanov, B. B. Chhun, S.-M. Guo, E. Hashemi, J. R. Byrum, J. A. Pérez-Bermejo, H. Wang, Y. Yu, P. G. Kazansky, B. R. Conklin, M. H. Han, and S. B. Mehta, "uPTI: uniaxial permittivity tensor imaging of intrinsic density and anisotropy," bioRxiv 2020.12.15.422951 (2020).
- ```
+Specifically, `waveorder` enables simulation and reconstruction of 2D or 3D:
 
-In addition to PTI, `waveorder` enables simulations and reconstructions of subsets of label-free measurements with subsets of the acquired data:
+1. __phase, projected retardance, and in-plane orientation__ from a polarization-diverse volumetric brightfield acquisition ([QLIPP](https://elifesciences.org/articles/55502)),
 
-1. Reconstruction of 2D or 3D phase, projected retardance, and in-plane orientation from a polarization-diverse volumetric brightfield acquisition ([QLIPP](https://elifesciences.org/articles/55502))
+2. __phase__ from a volumetric brightfield acquisition ([2D phase](https://www.osapublishing.org/ao/abstract.cfm?uri=ao-54-28-8566)/[3D phase](https://www.osapublishing.org/ao/abstract.cfm?uri=ao-57-1-a205)),
 
-2. Reconstruction of 2D or 3D phase from a volumetric brightfield acquisition ([2D](https://www.osapublishing.org/ao/abstract.cfm?uri=ao-54-28-8566)/[3D (PODT)](https://www.osapublishing.org/ao/abstract.cfm?uri=ao-57-1-a205) phase)
+3. __phase__ from an illumination-diverse volumetric acquisition ([2D](https://www.osapublishing.org/oe/fulltext.cfm?uri=oe-23-9-11394&id=315599)/[3D](https://www.osapublishing.org/boe/fulltext.cfm?uri=boe-7-10-3940&id=349951) differential phase contrast),
 
-3. Reconstruction of 2D or 3D phase from an illumination-diverse volumetric acquisition ([2D](https://www.osapublishing.org/oe/fulltext.cfm?uri=oe-23-9-11394&id=315599)/[3D](https://www.osapublishing.org/boe/fulltext.cfm?uri=boe-7-10-3940&id=349951) differential phase contrast)
+4. __fluorescence density__ from a widefield volumetric fluorescence acquisition (fluorescence deconvolution).  
 
-PTI provides volumetric reconstructions of mean permittivity ($\propto$ material density), differential permittivity ($\propto$ material anisotropy), 3D orientation, and optic sign. The following figure summarizes PTI acquisition and reconstruction with a small optical section of the mouse brain tissue:
+The [examples](https://github.com/mehta-lab/waveorder/tree/main/examples) demonstrate simulations and reconstruction for 2D QLIPP, 3D PODT, 3D fluorescence deconvolution, and 2D/3D PTI methods.
 
-![Data_flow](https://github.com/mehta-lab/waveorder/blob/main/readme.png?raw=true)
+If you are interested in deploying QLIPP, phase from brightfield, or fluorescence deconvolution for label-agnostic imaging at scale, checkout our [napari plugin](https://www.napari-hub.org/plugins/recOrder-napari),  [`recOrder-napari`](https://github.com/mehta-lab/recOrder).
 
+## Permittivity tensor imaging 
 
-The [examples](https://github.com/mehta-lab/waveorder/tree/main/examples) illustrate simulations and reconstruction for 2D QLIPP, 3D PODT, and 2D/3D PTI methods.
+Additionally, `waveorder` enabled the development of a new label-free imaging method, __permittivity tensor imaging (PTI)__, that measures density and  3D orientation of biomolecules with diffraction-limited resolution. These measurements are reconstructed from polarization-resolved images acquired with a sequence of oblique illuminations.
 
-If you are interested in deploying QLIPP or PODT for label-free imaging at scale, checkout our [napari plugin](https://www.napari-hub.org/plugins/recOrder-napari),  [`recOrder-napari`](https://github.com/mehta-lab/recOrder).
+The acquisition, calibration, background correction, reconstruction, and applications of PTI are described in the following [paper](https://doi.org/10.1101/2020.12.15.422951) published in Nature Methods:
 
-## Correlative imaging
+<details>
+<summary> Yeh et al. 2024 </summary>
+<pre><code>
+@article{yeh_2024,
+	author = {Yeh, Li-Hao and Ivanov, Ivan E. and Chandler, Talon and Byrum, Janie R. and Chhun, Bryant B. and Guo, Syuan-Ming and Foltz, Cameron and Hashemi, Ezzat and Perez-Bermejo, Juan A. and Wang, Huijun and Yu, Yanhao and Kazansky, Peter G. and Conklin, Bruce R. and Han, May H. and Mehta, Shalin B.},
+	title = {Permittivity tensor imaging: modular label-free imaging of 3D dry mass and 3D orientation at high resolution},
+	journal = {Nature Methods},
+	volume = {21},
+	number = {7},
+	pages = {1257--1274},
+	year = {2024},
+	month = jul,
+	issn = {1548-7105},
+	publisher = {Nature Publishing Group},
+	doi = {10.1038/s41592-024-02291-w}
+}
+</code></pre>
+</details>
 
-In addition to label-free reconstruction algorithms, `waveorder` also implements widefield fluorescence and fluorescence polarization reconstruction algorithms for correlative label-free and fluorescence imaging.
+PTI provides volumetric reconstructions of mean permittivity ($\propto$ material density), differential permittivity ($\propto$ material anisotropy), 3D orientation, and optic sign. The following figure summarizes PTI acquisition and reconstruction with a small optical section of the mouse brain tissue:
+
+![Data_flow](https://github.com/mehta-lab/waveorder/blob/main/readme.png?raw=true)
 
-1. Correlative measurements of biomolecular density and orientation from polarization-diverse widefield imaging ([multimodal Instant PolScope](https://opg.optica.org/boe/fulltext.cfm?uri=boe-13-5-3102&id=472350))
+## Examples
+The [examples](https://github.com/mehta-lab/waveorder/tree/main/examples) illustrate simulations and reconstruction for 2D QLIPP, 3D phase from brightfield, and 2D/3D PTI methods.
 
-We provide an [example notebook](https://github.com/mehta-lab/waveorder/blob/main/examples/documentation/fluorescence_deconvolution/fluorescence_deconv.ipynb) for widefield fluorescence deconvolution.
+If you are interested in deploying QLIPP or phase from brightbrield, or fluorescence deconvolution for label-agnostic imaging at scale, checkout our [napari plugin](https://www.napari-hub.org/plugins/recOrder-napari),  [`recOrder-napari`](https://github.com/mehta-lab/recOrder).
 
 ## Citation
 
@@ -113,10 +154,10 @@ Please cite this repository, along with the relevant preprint or paper, if you u
 
 ## Installation
 
-(Optional but recommended) install [anaconda](https://www.anaconda.com/products/distribution) and create a virtual environment:
+Create a virtual environment:
 
 ```sh
-conda create -y -n waveorder python=3.11
+conda create -y -n waveorder python=3.10
 conda activate waveorder
 ```
 
@@ -133,12 +174,11 @@ python
 >>> import waveorder
 ```
 
-(Optional) Download the repository, install `jupyter`, and experiment with the example notebooks
-
+(Optional) Install example dependencies, clone the repository, and run an example script:
 ```sh
+pip install waveorder[examples]
 git clone https://github.com/mehta-lab/waveorder.git
-pip install jupyter
-jupyter notebook ./waveorder/examples/
+python waveorder/examples/models/phase_thick_3d.py
 ```
 
 (M1 users) `pytorch` has [incomplete GPU support](https://github.com/pytorch/pytorch/issues/77764),

waveorder-2.2.1b0/README.md

@@ -0,0 +1,118 @@
+# waveorder
+
+[![Python package index](https://img.shields.io/pypi/v/waveorder.svg)](https://pypi.org/project/waveorder)
+[![PyPI monthly downloads](https://img.shields.io/pypi/dm/waveorder.svg)](https://pypistats.org/packages/waveorder)
+[![Total downloads](https://pepy.tech/badge/waveorder)](https://pepy.tech/project/waveorder)
+[![GitHub contributors](https://img.shields.io/github/contributors-anon/mehta-lab/waveorder)](https://github.com/mehta-lab/waveorder/graphs/contributors)
+![GitHub Repo stars](https://img.shields.io/github/stars/mehta-lab/waveorder)
+![GitHub forks](https://img.shields.io/github/forks/mehta-lab/waveorder)
+![PyPI - Python Version](https://img.shields.io/pypi/pyversions/waveorder)
+
+
+This computational imaging library enables wave-optical simulation and reconstruction of optical properties that report microscopic architectural order.
+
+## Computational label-agnostic imaging
+
+https://github.com/user-attachments/assets/4f9969e5-94ce-4e08-9f30-68314a905db6
+
+`waveorder` enables simulations and reconstructions of label-agnostic microscopy data as described in the following [preprint](https://arxiv.org/abs/2412.09775)
+<details>	
+<summary> Chandler et al. 2024 </summary>
+<pre><code>
+@article{chandler_2024,
+    author = {Chandler, Talon and Hirata-Miyasaki, Eduardo and Ivanov, Ivan E. and Liu, Ziwen and Sundarraman, Deepika and Ryan, Allyson Quinn and Jacobo, Adrian and Balla, Keir and Mehta, Shalin B.},
+	title = {waveOrder: generalist framework for label-agnostic computational microscopy},
+	journal = {arXiv},
+	year = {2024},
+	month = dec,
+	eprint = {2412.09775},
+	doi = {10.48550/arXiv.2412.09775}
+}
+</code></pre>
+</details>
+
+Specifically, `waveorder` enables simulation and reconstruction of 2D or 3D:
+
+1. __phase, projected retardance, and in-plane orientation__ from a polarization-diverse volumetric brightfield acquisition ([QLIPP](https://elifesciences.org/articles/55502)),
+
+2. __phase__ from a volumetric brightfield acquisition ([2D phase](https://www.osapublishing.org/ao/abstract.cfm?uri=ao-54-28-8566)/[3D phase](https://www.osapublishing.org/ao/abstract.cfm?uri=ao-57-1-a205)),
+
+3. __phase__ from an illumination-diverse volumetric acquisition ([2D](https://www.osapublishing.org/oe/fulltext.cfm?uri=oe-23-9-11394&id=315599)/[3D](https://www.osapublishing.org/boe/fulltext.cfm?uri=boe-7-10-3940&id=349951) differential phase contrast),
+
+4. __fluorescence density__ from a widefield volumetric fluorescence acquisition (fluorescence deconvolution).  
+
+The [examples](https://github.com/mehta-lab/waveorder/tree/main/examples) demonstrate simulations and reconstruction for 2D QLIPP, 3D PODT, 3D fluorescence deconvolution, and 2D/3D PTI methods.
+
+If you are interested in deploying QLIPP, phase from brightfield, or fluorescence deconvolution for label-agnostic imaging at scale, checkout our [napari plugin](https://www.napari-hub.org/plugins/recOrder-napari),  [`recOrder-napari`](https://github.com/mehta-lab/recOrder).
+
+## Permittivity tensor imaging 
+
+Additionally, `waveorder` enabled the development of a new label-free imaging method, __permittivity tensor imaging (PTI)__, that measures density and  3D orientation of biomolecules with diffraction-limited resolution. These measurements are reconstructed from polarization-resolved images acquired with a sequence of oblique illuminations.
+
+The acquisition, calibration, background correction, reconstruction, and applications of PTI are described in the following [paper](https://doi.org/10.1101/2020.12.15.422951) published in Nature Methods:
+
+<details>
+<summary> Yeh et al. 2024 </summary>
+<pre><code>
+@article{yeh_2024,
+	author = {Yeh, Li-Hao and Ivanov, Ivan E. and Chandler, Talon and Byrum, Janie R. and Chhun, Bryant B. and Guo, Syuan-Ming and Foltz, Cameron and Hashemi, Ezzat and Perez-Bermejo, Juan A. and Wang, Huijun and Yu, Yanhao and Kazansky, Peter G. and Conklin, Bruce R. and Han, May H. and Mehta, Shalin B.},
+	title = {Permittivity tensor imaging: modular label-free imaging of 3D dry mass and 3D orientation at high resolution},
+	journal = {Nature Methods},
+	volume = {21},
+	number = {7},
+	pages = {1257--1274},
+	year = {2024},
+	month = jul,
+	issn = {1548-7105},
+	publisher = {Nature Publishing Group},
+	doi = {10.1038/s41592-024-02291-w}
+}
+</code></pre>
+</details>
+
+PTI provides volumetric reconstructions of mean permittivity ($\propto$ material density), differential permittivity ($\propto$ material anisotropy), 3D orientation, and optic sign. The following figure summarizes PTI acquisition and reconstruction with a small optical section of the mouse brain tissue:
+
+![Data_flow](https://github.com/mehta-lab/waveorder/blob/main/readme.png?raw=true)
+
+## Examples
+The [examples](https://github.com/mehta-lab/waveorder/tree/main/examples) illustrate simulations and reconstruction for 2D QLIPP, 3D phase from brightfield, and 2D/3D PTI methods.
+
+If you are interested in deploying QLIPP or phase from brightbrield, or fluorescence deconvolution for label-agnostic imaging at scale, checkout our [napari plugin](https://www.napari-hub.org/plugins/recOrder-napari),  [`recOrder-napari`](https://github.com/mehta-lab/recOrder).
+
+## Citation
+
+Please cite this repository, along with the relevant preprint or paper, if you use or adapt this code. The citation information can be found by clicking "Cite this repository" button in the About section in the right sidebar.
+
+## Installation
+
+Create a virtual environment:
+
+```sh
+conda create -y -n waveorder python=3.10
+conda activate waveorder
+```
+
+Install `waveorder` from PyPI:
+
+```sh
+pip install waveorder
+```
+
+Use `waveorder` in your scripts:
+
+```sh
+python
+>>> import waveorder
+```
+
+(Optional) Install example dependencies, clone the repository, and run an example script:
+```sh
+pip install waveorder[examples]
+git clone https://github.com/mehta-lab/waveorder.git
+python waveorder/examples/models/phase_thick_3d.py
+```
+
+(M1 users) `pytorch` has [incomplete GPU support](https://github.com/pytorch/pytorch/issues/77764),
+so please use `export PYTORCH_ENABLE_MPS_FALLBACK=1`
+to allow some operators to fallback to CPU
+if you plan to use GPU acceleration for polarization reconstruction. 

waveorder-2.2.1b0/examples/README.md

@@ -0,0 +1,10 @@
+`waveorder` is undergoing a significant refactor, and this `examples/` folder serves as a good place to understand the current state of the repository.
+
+Some examples require `pip install waveorder[examples]` for `napari` and `jupyter`. Visit the [napari installation guide](https://napari.org/dev/tutorials/fundamentals/installation.html) if napari installation fails.
+
+| Folder      | Requires                   | Description                                                                                           |
+|------------------|----------------------------|-------------------------------------------------------------------------------------------------------|
+| `models/`        | `pip install waveorder[examples]`      | Demonstrates the latest functionality of `waveorder` through simulations and reconstructions using various models. |
+| `maintenance/`   | `pip install waveorder`                | Examples of computational imaging methods enabled by functionality of waveorder; scripts are maintained with automated tests.               |
+| `visuals/`       | `pip install waveorder[examples]`      | Visualizations of transfer functions and Green's tensors.                                    |
+| `documentation/` | `pip install waveorder`, complete datasets | Provides examples of real-data reconstructions; serves as documentation and is not actively maintained. |