Add Additional Citations to Ref page

doc/references.rst

@@ -20,14 +20,17 @@ If you use one of the following preprocessing methods, please cite the appropria
 - :code:`common_reference` [Rolston]_
 
 Motion Correction
-^^^^^^^^^^^^^^^^^
+-----------------
 If you use the :code:`correct_motion` method in the preprocessing module, please cite [Garcia]_
 as well as the references that correspond to the :code:`preset` you used:
 
-- :code:`nonrigid_accurate` [Windolf]_ [Varol]_
-- :code:`nonrigid_fast_and_accurate` [Windolf]_ [Varol]_ [Pachitariu]_
+- :code:`nonrigid_accurate` [Windolf_a]_ [Varol]_
+- :code:`nonrigid_fast_and_accurate` [Windolf_a]_ [Varol]_ [Pachitariu]_
 - :code:`rigid_fast` *no additional citation needed*
 - :code:`kilosort_like` [Pachitariu]_
+- :code:`dredge_ap` [Windolf_b]_
+- :code:`dredge_lfp` [Windolf_b]_
+- :code:`medicine` [Watters]_
 
 Sorters Module
 --------------
@@ -47,7 +50,14 @@ please include the appropriate citation for the :code:`sorter_name` parameter yo
 Postprocessing Module
 ---------------------
 
-If you use the :code:`acgs_3d` extensions, (i.e. :code:`postprocessing.compute_acgs_3d`, :code:`postprocessing.ComputeACG3D`) please cite [Beau]_
+If you use the :code:`postprocessing module`, i.e. you use the :code:`analyzer.compute()` include the citations for the following
+methods:
+
+ - :code:`acgs_3d` [Beau]_
+ - :code:`unit_locations` or :code:`spike_locations` with :code:`monopolar_triangulation` based on work from [Boussard]_
+ - :code:`unit_locations` or :code:`spike_locations` with :code:`grid_convolution` based on work from [Pachitariu]_
+ - :code:`template_metrics` [Jia]_
+
 
 Qualitymetrics Module
 ---------------------
@@ -74,15 +84,20 @@ important for your research:
 - :code:`nearest_neighbor` or :code:`nn_isolation` or :code:`nn_noise_overlap` [Chung]_ [Siegle]_
 - :code:`silhouette`  [Rousseeuw]_ [Hruschka]_
 
+
 Curation Module
 ---------------
 If you use the :code:`get_potential_auto_merge` method from the curation module, please cite [Llobet]_
 
+If you use :code:`auto_label_units` or :code:`train_model`, please cite [Jain]_
+
 References
 ----------
 
 .. [Beau] `A deep learning strategy to identify cell types across species from high-density extracellular recordings. 2025. <https://doi.org/10.1016/j.cell.2025.01.041>`_
 
+.. [Boussard] `Three-dimensional spike localization and imporved motion correction for Neuropixels recordings. 2021 <https://www.biorxiv.org/content/10.1101/2021.11.05.467503v1>`_
+
 .. [Buccino] `SpikeInterface, a unified framework for spike sorting. 2020. <https://pubmed.ncbi.nlm.nih.gov/33170122/>`_
 
 .. [Buzsáki] `The Log-Dynamic Brain: How Skewed Distributions Affect Network Operations. 2014. <https://pubmed.ncbi.nlm.nih.gov/24569488/>`_
@@ -107,7 +122,11 @@ References
 
 .. [IBL] `Spike sorting pipeline for the International Brain Laboratory. 2022. <https://figshare.com/articles/online_resource/Spike_sorting_pipeline_for_the_International_Brain_Laboratory/19705522/3>`_
 
-.. [Jackson] Quantitative assessment of extracellular multichannel recording quality using measures of cluster separation. Society of Neuroscience Abstract. 2005.
+.. [Jackson] `Quantitative assessment of extracellular multichannel recording quality using measures of cluster separation. Society of Neuroscience Abstract. 2005. <https://www.sciencedirect.com/science/article/abs/pii/S0306452204008425>`_
+
+.. [Jain] `UnitRefine: A Community Toolbox for Automated Spike Sorting Curation. 2025 <https://www.biorxiv.org/content/10.1101/2025.03.30.645770v1>`_
+
+.. [Jia] `High-density extracellular probes reveal dendritic backpropagation and facilitate neuron classification. 2019 <https://journals.physiology.org/doi/full/10.1152/jn.00680.2018>`_
 
 .. [Lee] `YASS: Yet another spike sorter. 2017. <https://www.biorxiv.org/content/10.1101/151928v1>`_
 
@@ -119,7 +138,7 @@ References
 
 .. [Niediek] `Reliable Analysis of Single-Unit Recordings from the Human Brain under Noisy Conditions: Tracking Neurons over Hours. 2016. <https://pubmed.ncbi.nlm.nih.gov/27930664/>`_
 
-.. [npyx] `NeuroPyxels: loading, processing and plotting Neuropixels data in python. 2021. <https://doi.org/10.5281/zenodo.5509776>_`
+.. [npyx] `NeuroPyxels: loading, processing and plotting Neuropixels data in python. 2021. <https://doi.org/10.5281/zenodo.5509776>`_
 
 .. [Pachitariu] `Spike sorting with Kilosort4. 2024. <https://pubmed.ncbi.nlm.nih.gov/38589517/>`_
 
@@ -137,6 +156,10 @@ References
 
 .. [Varol] `Decentralized Motion Inference and Registration of Neuropixel Data. 2021. <https://ieeexplore.ieee.org/document/9414145>`_
 
-.. [Windolf] `Robust Online Multiband Drift Estimation in Electrophysiology Data. 2022. <https://www.biorxiv.org/content/10.1101/2022.12.04.519043v2>`_
+.. [Watters] `MEDiCINe: Motion Correction for Neural Electrophysiology Recordings. 2025. <https://www.eneuro.org/content/12/3/ENEURO.0529-24.2025>`_
+
+.. [Windolf_a] `Robust Online Multiband Drift Estimation in Electrophysiology Data. 2022. <https://www.biorxiv.org/content/10.1101/2022.12.04.519043v2>`_
+
+.. [Windolf_b] `DREDge: robust motion correction for high-density extracellular recordings across species. 2023 <https://www.biorxiv.org/content/10.1101/2023.10.24.563768v1>`_
 
 .. [Yger] `A spike sorting toolbox for up to thousands of electrodes validated with ground truth recordings in vitro and in vivo. 2018. <https://pubmed.ncbi.nlm.nih.gov/29557782/>`_