address missing DOIs and add citation info

choosehappy · May 30, 2024 · 35e9908 · 35e9908
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diff --git a/CITATION.cff b/CITATION.cff
@@ -0,0 +1,27 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it using the following information."
+authors:
+  - family-names: Liakopoulos
+    given-names: Petros
+  - family-names: Massonnet
+    given-names: Julien
+  - family-names: Bonjour
+    given-names: Jonatan
+  - family-names: Mizrakli
+    given-names: Medya Tekes
+  - family-names: Graham
+    given-names: Simon
+  - family-names: Cuendet
+    given-names: Michel A
+  - family-names: Seipel
+    given-names: Amanda H
+  - family-names: Michielin
+    given-names: Olivier
+  - family-names: Merkler
+    given-names: Doron
+  - family-names: Janowczyk
+    given-names: Andrew
+title: "HoverFast: an accurate, high-throughput, clinically deployable nuclear segmentation tool for brightfield digital pathology images"
+version: 1.0.0
+date-released: 2024-05-30
+url: "https://arxiv.org/abs/2405.14028"
diff --git a/README.md b/README.md
@@ -11,7 +11,7 @@ Welcome to the official repository of HoverFast, a high-performance tool designe
 
 ## Overview
 
-HoverFast utilizes advanced computational methods to facilitate rapid and accurate segmentation of nuclei within large histopathological images, supporting research and diagnostics in medical imaging.
+HoverFast utilizes advanced computational methods to facilitate rapid and accurate segmentation of nuclei within large histopathological images, supporting research and diagnostics in medical imaging. For more info on the inner workings of HoverFast, do not hesitate to go over our [preprint](https://arxiv.org/abs/2405.14028)
 
 ## Documentation
 
@@ -178,6 +178,23 @@ pytest -vv
 ```
 Note that the first time you run these, the infer_wsi test can take longer since the slide will be downloaded locally
 
+For more detailed instructions, including setting up your environment and running specific tests, please refer to the [testing documentation](https://hoverfast.readthedocs.io/en/latest/unit_testing.html)
+
+## How to Cite HoverFast
+
+If you use HoverFast in your research, please cite our paper:
+
+```bibtex
+@article{liakopoulos2024hoverfast,
+  title={HoverFast: an accurate, high-throughput, clinically deployable nuclear segmentation tool for brightfield digital pathology images},
+  author={Liakopoulos, Petros and Massonnet, Julien and Bonjour, Jonatan and Mizrakli, Medya Tekes and Graham, Simon and Cuendet, Michel A and Seipel, Amanda H and Michielin, Olivier and Merkler, Doron and Janowczyk, Andrew},
+  journal={arXiv preprint arXiv:2405.14028},
+  year={2024}
+}
+```
+By citing HoverFast, you help us to continue our research and development. Thank you for your support!
+
+
 ## Authors
 
 - **Julien Massonnet** - [JulienMassonnet](https://github.com/JulienMassonnet)

diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -38,9 +38,4 @@ For that reason, we highly recommend looking into other tools such as HistoQC (h
    training
    unit_testing
 
-Indices and tables
-==================
 
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
diff --git a/paper/paper.bib b/paper/paper.bib
@@ -25,6 +25,7 @@ @article{stringer2021cellpose
   number={1},
   pages={100--106},
   year={2021},
+  doi={10.1038/s41592-020-01018-x},
   publisher={Nature Publishing Group US New York}}
 
 @article{graham2019hover,
@@ -34,6 +35,7 @@ @article{graham2019hover
   volume={58},
   pages={101563},
   year={2019},
+  doi={10.1016/j.media.2019.101563},
   publisher={Elsevier}}
 
 @article{bankhead2017qupath,
@@ -44,6 +46,7 @@ @article{bankhead2017qupath
   number={1},
   pages={1--7},
   year={2017},
+  doi={10.1038/s41598-017-17204-5},
   publisher={Nature Publishing Group}}
 
 @article{su2021msu,
@@ -53,6 +56,7 @@ @article{su2021msu
   volume={12},
   pages={639930},
   year={2021},
+  doi={10.3389/fgene.2021.639930},
   publisher={Frontiers Media SA}}
 
 @article{paszke2017automatic,
@@ -66,7 +70,9 @@ @article{scikit-learn
   journal={Journal of Machine Learning Research}, 
   volume={12}, 
   pages={2825--2830}, 
-  year={2011}}
+  year={2011}},
+  url={http://jmlr.org/papers/v12/pedregosa11a.html},
+  }
 
 @article{opencv_library,
   author = {Bradski, G.},
@@ -86,6 +92,7 @@ @article{weinstein2013cancer
   number={10},
   pages={1113--1120},
   year={2013},
+  doi={10.1038/ng.2764}
   publisher={Nature Publishing Group}}
 
 @article{hinton2015distilling,  
@@ -97,7 +104,9 @@ @article{hinton2015distilling
 @article{hu2022teacher,
   title={Teacher-student architecture for knowledge learning: A survey},  
   author={Hu, Chengming and Li, Xuan and Liu, Dan and Chen, Xi and Wang, Ju and Liu, Xue},
-  journal={arXiv preprint arXiv:2210.17332},  year={2022}}
+  journal={arXiv preprint arXiv:2210.17332},
+  year={2022},
+  }
 
 @article{janowczyk2019histoqc,
   title={HistoQC: an open-source quality control tool for digital pathology slides},
@@ -106,7 +115,8 @@ @article{janowczyk2019histoqc
   volume={3},
   pages={1--7},
   year={2019},
-  publisher={American Society of Clinical Oncology}
+  doi={10.1200/CCI.18.00157},
+  publisher={American Society of Clinical Oncology},
   }