diff --git a/doc/references.rst b/doc/references.rst index 6ba6efe6a1..e4b23f1b76 100644 --- a/doc/references.rst +++ b/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. `_ +.. [Boussard] `Three-dimensional spike localization and imporved motion correction for Neuropixels recordings. 2021 `_ + .. [Buccino] `SpikeInterface, a unified framework for spike sorting. 2020. `_ .. [Buzsáki] `The Log-Dynamic Brain: How Skewed Distributions Affect Network Operations. 2014. `_ @@ -107,7 +122,11 @@ References .. [IBL] `Spike sorting pipeline for the International Brain Laboratory. 2022. `_ -.. [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. `_ + +.. [Jain] `UnitRefine: A Community Toolbox for Automated Spike Sorting Curation. 2025 `_ + +.. [Jia] `High-density extracellular probes reveal dendritic backpropagation and facilitate neuron classification. 2019 `_ .. [Lee] `YASS: Yet another spike sorter. 2017. `_ @@ -119,7 +138,7 @@ References .. [Niediek] `Reliable Analysis of Single-Unit Recordings from the Human Brain under Noisy Conditions: Tracking Neurons over Hours. 2016. `_ -.. [npyx] `NeuroPyxels: loading, processing and plotting Neuropixels data in python. 2021. _` +.. [npyx] `NeuroPyxels: loading, processing and plotting Neuropixels data in python. 2021. `_ .. [Pachitariu] `Spike sorting with Kilosort4. 2024. `_ @@ -137,6 +156,10 @@ References .. [Varol] `Decentralized Motion Inference and Registration of Neuropixel Data. 2021. `_ -.. [Windolf] `Robust Online Multiband Drift Estimation in Electrophysiology Data. 2022. `_ +.. [Watters] `MEDiCINe: Motion Correction for Neural Electrophysiology Recordings. 2025. `_ + +.. [Windolf_a] `Robust Online Multiband Drift Estimation in Electrophysiology Data. 2022. `_ + +.. [Windolf_b] `DREDge: robust motion correction for high-density extracellular recordings across species. 2023 `_ .. [Yger] `A spike sorting toolbox for up to thousands of electrodes validated with ground truth recordings in vitro and in vivo. 2018. `_