Merge pull request #90 from jono3030/jo-dev-225-rst_docs_fork

[PR] merge rst version of docs

README.md

@@ -1,7 +1,7 @@
 [![GitHub license](https://img.shields.io/github/license/mgoubran/MIRACL)](https://github.com/mgoubran/MIRACL/blob/master/LICENSE.md) ![Docker Pulls](https://img.shields.io/docker/pulls/mgoubran/miracl)
 
 <p align="center">
-  <img src="docs/gallery/icon.png" alt="alt text" width="400" height="250"/>
+  <img src="docs/gallery/images/icon.png" alt="alt text" width="400" height="250"/>
 </p>
 
 ___

docs/_static/css/custom.css

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+/* Increase maximum width of help document */
+.wy-nav-content {
+    max-width: 1100px !important;
+}
+
+/* override table width restrictions */
+@media screen and (min-width: 767px) {
+
+  .wy-table-responsive table td {
+    /* !important prevents the common CSS stylesheets from
+       overriding this as on RTD they are loaded after this stylesheet */
+    white-space: normal !important;
+  }
+
+  .wy-table-responsive {
+    overflow: visible !important;
+  }
+
+}
+
+/* Round borders of GitHub logos */
+.sphinx-contributors img {
+    border-radius: 50%;
+}
+
+/* Tests */
+
+/* .wy-nav-content { */
+/*     max-width: 125% !important; */
+/* } */
+
+/* .wy-nav-side { */
+/*     max-width: 25% !important; */
+/* } */
+
+/* @media screen and (max-width: 950px){ */
+/*     .wy-body-for-nav{background:#fcfcfc} */
+/*     .wy-nav-top{display:block} */
+/*     .wy-nav-side{left:-300px} */
+/*     .wy-nav-side.shift{width:85%;left:0} */
+/*     .wy-side-scroll{width:auto} */
+/*     .wy-side-nav-search{width:auto} */
+/*     .wy-menu.wy-menu-vertical{width:auto} */
+/*     .wy-nav-content-wrap{margin-left:0} */
+/*     .wy-nav-content-wrap */
+/*     .wy-nav-content{padding:1.618em} */
+/*     .wy-nav-content-wrap.shift{position:fixed;min-width:100%;left:85%;top:0;height:100%;overflow:hidden} */
+/* } */
+

docs/about/acknowledgements.rst

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+Acknowledgements
+################
+
+Huge thank you to:
+
+- Vanessa Sochat (@vsoch) for creating the Docker & Singularity containers for 
+  the pipeline
+- Newton Cho, Jordan Squair and Stéphane Pagès for helping optimize the 
+  segmentation workflows & troubleshooting
+- The members of `AICONS Lab <https://aiconslab.github.io/>`_ for their 
+  feedback and contributions
+
+GitHub contributers (ordered by number of commits):
+
+.. contributors:: AICONSlab/MIRACL
+    :exclude: mgoubran,entiri,jono3030
+    :avatars:
+    :order: DESC
+
+PR's:
+
+- `dariocalvarez <https://github.com/DarioCAlvarez>`_

docs/about/citations.rst

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+MIRACL in research
+##################
+
+A selection of publications that used or referenced :program:`MIRACL`:
+
+Hsueh, B., Chen, R., Jo, Y., Tang, D., Raffiee, M., Kim, Y. S., ... Goubran, 
+M., & Deisseroth, K. (2023). `Cardiogenic control of affective behavioural 
+state <https://www.nature.com/articles/s41586-023-05748-8>`_. Nature, 1-8.
+
+Qu, L., Li, Y., Xie, P., Liu, L., Wang, Y., Wu, J., ... & Peng, H. (2022). 
+`Cross-modal coherent registration of whole mouse brains
+<https://www.nature.com/articles/s41592-021-01334-w>`_. Nature Methods, 19(1), 
+111-118.
+
+Georgiadis, M., Schroeter, A., Gao, Z., Guizar-Sicairos, M., Liebi, M., Leuze, 
+C., ... & Rudin, M. (2021). `Nanostructure-specific X-ray tomography reveals 
+myelin levels, integrity and axon orientations in mouse and human nervous 
+tissue <https://www.nature.com/articles/s41467-021-22719-7>`_. Nature 
+communications, 12(1), 2941.
+
+Wang, X., Zeng, W., Yang, X., Zhang, Y., Fang, C., Zeng, S., ... & Fei, P. 
+(2021). `Bi-channel image registration and deep-learning segmentation (BIRDS) 
+for efficient, versatile 3D mapping of mouse brain 
+<https://elifesciences.org/articles/63455.pdf>`_. Elife, 10, e63455.
+
+Boillat, M., Hammoudi, P. M., Dogga, S. K., Pages, S., Goubran, M., Rodriguez,
+I., & Soldati-Favre, D. (2020). `Neuroinflammation-associated aspecific 
+manipulation of mouse predator fear by Toxoplasma gondii 
+<https://www.sciencedirect.com/science/article/pii/S2211124719316699>`_. Cell 
+reports, 30(2), 320-334.
+
+Pallast, N., Wieters, F., Nill, M., Fink, G. R., & Aswendt, M. (2020). `Graph 
+theoretical quantification of white matter reorganization after cortical 
+stroke in mice
+<https://www.sciencedirect.com/science/article/pii/S1053811920303591>`_. 
+NeuroImage, 217, 116873.
+
+Ito, M., Aswendt, M., Lee, A. G., Ishizaka, S., Cao, Z., Wang, E. H., ... & 
+Steinberg, G. K. (2018). `RNA-sequencing analysis revealed a distinct motor 
+cortex transcriptome in spontaneously recovered mice after stroke
+<https://www.ahajournals.org/doi/full/10.1161/STROKEAHA.118.021508>`_. Stroke, 
+49(9), 2191-2199.

docs/about/citing.rst

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+Citing MIRACL
+#############
+
+Citation guidelines for using MIRACL in your work.
+
+MIRACL publication
+==================
+
+If you use :program:`MIRACL` in your work please cite our 
+`paper <https://www.nature.com/articles/s41467-019-13374-0>`_:
+
+APA
+---
+
+Goubran, M., Leuze, C., Hsueh, B., Aswendt, M., Ye, L., Tian, Q., Cheng, M.Y., 
+Crow, A., Steinberg, G.K., McNab, J.A., Deisseroth, K., and Zeineh, M. (2019). 
+`Multimodal image registration and connectivity analysis for integration of 
+connectomic data from microscopy to MRI <https://www.nature.com/articles/s41467-019-13374-0>`_. 
+Nature communications, 10(1), 5504.
+
+BibTeX
+------
+
+.. code-block::
+
+   @article{goubran2019multimodal,
+     title={Multimodal image registration and connectivity analysis for integration of connectomic data from microscopy to MRI},
+     author={Goubran, Maged and Leuze, Christoph and Hsueh, Brian and Aswendt, Markus and Ye, Li and Tian, Qiyuan and Cheng, Michelle Y and Crow, Ailey and Steinberg, Gary K and McNab, Jennifer A and Deisseroth, Karl and Zeineh, Michael},
+     journal={Nature communications},
+     volume={10},
+     number={1},
+     pages={5504},
+     year={2019},
+     publisher={Nature Publishing Group UK London}
+   }
+
+Tools used by MIRACL
+====================
+
+Some of our functions build on or use these tools (please cite their work if 
+you are using them):
+
+=================================================================  ========================
+Tool 	                                                             Function
+=================================================================  ========================
+`Allen Regional Atlas <http://mouse.brain-map.org/static/atlas>`_  Atlas registration
+`Allen Connectivity Atlas <http://connectivity.brain-map.org/>`_   Connectivity analyses
+`ANTs <https://github.com/stnava/ANTs>`_ 	                         Registration
+`Fiji <https://imagej.nih.gov/ij/index.html>`_ 	                   Segmentation
+`c3d <https://sourceforge.net/projects/c3d>`_ 	                   Image processing
+`FSL <https://fsl.fmrib.ox.ac.uk/fsl/fslwiki>`_ 	                 Diffusion MRI processing
+`MRtrix3 <https://mrtrix.readthedocs.io/en/latest/>`_ 	           Tractography
+`TrackVis/DTK <http://trackvis.org/>`_ 	                           Tractography
+=================================================================  ========================