add initial joss files

codemeta.json

@@ -0,0 +1,23 @@
+{
+  "@context": "https://raw.githubusercontent.com/codemeta/codemeta/master/codemeta.jsonld",
+  "@type": "Code",
+  "author": [
+    {
+      "@id": "0000-0003-2882-2471",
+      "@type": "Person",
+      "email": "[email protected]",
+      "name": "Nicholas M. Anthony",
+      "affiliation": "Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA."
+    }
+  ],
+  "identifier": "",
+  "codeRepository": "https://github.com/nanthony21/PWSpy",
+  "datePublished": "2021-11-09",
+  "dateModified": "2021-11-09",
+  "dateCreated": "2021-11-09",
+  "description": "A Python library dedicated to the analysis of Partial Wave Spectroscopic Microscopy data.",
+  "keywords": "Python, Microscopy, Hyperspectral Imaging",
+  "license": "GPS v3.0",
+  "title": "PWSpy",
+  "version": "1.0.0"
+}

paper.bib

@@ -0,0 +1,20 @@
+
+@article{cherkezyan_zhang_subramanian_capoglu_taflove_backman_2017,
+    title={Review of interferometric spectroscopy of scattered light for the quantification of subdiffractional structure of biomaterials},
+    volume={22},
+    DOI={10.1117/1.jbo.22.3.030901},
+    number={3},
+    journal={Journal of Biomedical Optics},
+    author={Cherkezyan, Lusik and Zhang, Di and Subramanian, Hariharan and Capoglu, Ilker and Taflove, Allen and Backman, Vadim},
+    year={2017},
+    pages={030901}}
+
+@article{li_eshein_virk_eid_vanderway_frederick_bleher_szleifer_dravid_backman_et_al._2020,
+    title={Nanoscale Chromatin Imaging and Analysis (nano-ChIA) Platform Bridges 4-D Chromatin Organization with Molecular Function},
+    volume={26},
+    DOI={10.1017/s1431927620016785},
+    number={S2},
+    journal={Microscopy and Microanalysis},
+    author={Li, Yue and Eshein, Adam and Virk, Ranya and Eid, Aya and Vanderway, David and Frederick, Jane and Bleher, Reiner and Szleifer, Igal and Dravid, Vinayak and Backman, Vadim and et al.},
+    year={2020},
+    pages={1046–1050}}

paper.md

@@ -0,0 +1,97 @@
+---
+title: 'PWSpy: A Python library dedicated to the analysis of Partial Wave Spectroscopic Microscopy data.'
+tags:
+ - Python
+ - Microscopy
+ - Hyperspectral Imaging
+authors:
+ - name: Nicholas M. Anthony
+   orcid: 0000-0003-2882-2471
+   affiliation: 1
+affiliations:
+ - name: Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA.
+
+date: 10 November 2021
+bibliography: paper.bib
+---
+
+# Summary
+
+The forces on stars, galaxies, and dark matter under external gravitational
+fields lead to the dynamical evolution of structures in the universe. The orbits
+of these bodies are therefore key to understanding the formation, history, and
+future state of galaxies. The field of "galactic dynamics," which aims to model
+the gravitating components of galaxies to study their structure and evolution,
+is now well-established, commonly taught, and frequently used in astronomy.
+Aside from toy problems and demonstrations, the majority of problems require
+efficient numerical tools, many of which require the same base code (e.g., for
+performing numerical orbit integration).
+
+# Statement of need
+
+`Gala` is an Astropy-affiliated Python package for galactic dynamics. Python
+enables wrapping low-level languages (e.g., C) for speed without losing
+flexibility or ease-of-use in the user-interface. The API for `Gala` was
+designed to provide a class-based and user-friendly interface to fast (C or
+Cython-optimized) implementations of common operations such as gravitational
+potential and force evaluation, orbit integration, dynamical transformations,
+and chaos indicators for nonlinear dynamics. `Gala` also relies heavily on and
+interfaces well with the implementations of physical units and astronomical
+coordinate systems in the `Astropy` package [@astropy] (`astropy.units` and
+`astropy.coordinates`).
+
+`Gala` was designed to be used by both astronomical researchers and by
+students in courses on gravitational dynamics or astronomy. It has already been
+used in a number of scientific publications [@Pearson:2017] and has also been
+used in graduate courses on Galactic dynamics to, e.g., provide interactive
+visualizations of textbook material [@Binney:2008]. The combination of speed,
+design, and support for Astropy functionality in `Gala` will enable exciting
+scientific explorations of forthcoming data releases from the *Gaia* mission
+[@gaia] by students and experts alike.
+
+# Mathematics
+
+Single dollars ($) are required for inline mathematics e.g. $f(x) = e^{\pi/x}$
+
+Double dollars make self-standing equations:
+
+$$\Theta(x) = \left\{\begin{array}{l}
+0\textrm{ if } x < 0\cr
+1\textrm{ else}
+\end{array}\right.$$
+
+You can also use plain \LaTeX for equations
+\begin{equation}\label{eq:fourier}
+\hat f(\omega) = \int_{-\infty}^{\infty} f(x) e^{i\omega x} dx
+\end{equation}
+and refer to \autoref{eq:fourier} from text.
+
+# Citations
+
+Citations to entries in paper.bib should be in
+[rMarkdown](http://rmarkdown.rstudio.com/authoring_bibliographies_and_citations.html)
+format.
+
+If you want to cite a software repository URL (e.g. something on GitHub without a preferred
+citation) then you can do it with the example BibTeX entry below for @fidgit.
+
+For a quick reference, the following citation commands can be used:
+- `@author:2001`  ->  "Author et al. (2001)"
+- `[@author:2001]` -> "(Author et al., 2001)"
+- `[@author1:2001; @author2:2001]` -> "(Author1 et al., 2001; Author2 et al., 2002)"
+
+# Figures
+
+Figures can be included like this:
+![Caption for example figure.\label{fig:example}](figure.png)
+and referenced from text using \autoref{fig:example}.
+
+Figure sizes can be customized by adding an optional second parameter:
+![Caption for example figure.](figure.png){ width=20% }
+
+# Acknowledgements
+
+We acknowledge contributions from Brigitta Sipocz, Syrtis Major, and Semyeong
+Oh, and support from Kathryn Johnston during the genesis of this project.
+
+# References