From 7629c2e751e2809e2749886cbbe7ea0208737d45 Mon Sep 17 00:00:00 2001
From: Jordao Bragantini <jordao.bragantini@czbiohub.org>
Date: Tue, 11 Jun 2024 17:43:54 -0700
Subject: [PATCH] add citation

---
 README.md             |  6 +++++-
 docs/source/api.rst   |  1 -
 docs/source/index.rst | 20 ++++++++++++++++++++
 3 files changed, 25 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index fb74b8c..06bb8ba 100644
--- a/README.md
+++ b/README.md
@@ -92,8 +92,10 @@ Depending on the operating system, the gurobi library might be missing and you n
 
 ## Citing
 
+If you use ultrack in your research, please cite the following paper:
+
 ```
-@misc{bragantini2023ultrack,
+@misc{bragantini2023ucmtracking,
       title={Large-Scale Multi-Hypotheses Cell Tracking Using Ultrametric Contours Maps},
       author={Jordão Bragantini and Merlin Lange and Loïc Royer},
       year={2023},
@@ -102,3 +104,5 @@ Depending on the operating system, the gurobi library might be missing and you n
       primaryClass={cs.CV}
 }
 ```
+
+And the respective auxiliary methods (e.g. Cellpose, napari, etc) depending on your usage.
diff --git a/docs/source/api.rst b/docs/source/api.rst
index 928a6e1..41ea211 100644
--- a/docs/source/api.rst
+++ b/docs/source/api.rst
@@ -43,7 +43,6 @@ Core functionalities
 ====================
 
 .. include:: ../../ultrack/core/README.md
-    :parser: myst
 
 .. automodule:: ultrack
     :members:
diff --git a/docs/source/index.rst b/docs/source/index.rst
index c9cba1a..1fc8152 100644
--- a/docs/source/index.rst
+++ b/docs/source/index.rst
@@ -54,6 +54,26 @@ Zebrafish imaged using `DaXi <https://www.nature.com/articles/s41592-022-01417-2
 
 .. include:: theory.rst
 
+
+Citing
+------
+
+If you use ``ultrack`` in your research, please cite the following paper:
+
+.. code-block:: bibtex
+
+   @article{bragantini2023ucmtracking,
+      title={Large-Scale Multi-Hypotheses Cell Tracking Using Ultrametric Contours Maps},
+      author={Jordão Bragantini and Merlin Lange and Loïc Royer},
+      year={2023},
+      eprint={2308.04526},
+      archivePrefix={arXiv},
+      primaryClass={cs.CV}
+   }
+
+And the respective auxiliary methods (e.g. Cellpose, napari, etc) depending on your usage.
+
+
 Documentation contents
 ``````````````````````