Merge pull request #396 from sytseng/main

Add visualize_2p_VR_behavior notebook
AllenInstitute · Jun 12, 2024 · fbb153a · fbb153a
2 parents 960ff48 + 74a39bd
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diff --git a/README.md b/README.md
@@ -40,7 +40,7 @@ We are releasing this code to the public as a tool we expect others to use and a
 - [Neural dynamics using time-analysis with CEBRA](https://alleninstitute.github.io/openscope_databook/higher-order/cebra_time.html)  
   [CEBRA Demo on the CEBRA Repository](https://github.com/adaptivemotorcontrollab/CEBRA-demos/blob/main/Demo_openscope_databook.ipynb)
 - [Extracting clusters of correlated neurons with TCA](https://alleninstitute.github.io/openscope_databook/higher-order/tca.html)
-- [Estimating behavioral state given trial choices and relating states to pupil size](https://alleninstitute.github.io/openscope_databook/higher-order/behavioral_state.ipynb)
+- [Estimating behavioral state given trial choices and relating states to pupil size](https://alleninstitute.github.io/openscope_databook/higher-order/behavioral_state.html)
 - Analysis of functional connectivity.
 
 ### Chapter 5: Replicating figures

diff --git a/docs/references.bib b/docs/references.bib
@@ -205,4 +205,15 @@ @article{Vonderheydt1984
 ,   pages	= {}
 ,   publisher = {Society for Neuroscience}
 ,   url     = {https://doi.org/10.1523/JNEUROSCI.09-05-01731.1989}
-}
+}
+@article{Tseng2022
+,   title   = {Shared and specialized coding across posterior cortical areas for dynamic navigation decisions}
+,   author  = {Shih-Yi Tseng and Selmaan N. Chettih and Charlotte Arlt and Roberto Barroso-Luque and Christopher D. Harvey}
+,   journal = {Neuron}
+,   year    = {2022}
+,   volume	= {110}
+,   number	= {15}
+,   pages	= {2484-2502}
+,   publisher = {Elsevier}
+,   url     = {https://doi.org/10.1016/j.neuron.2022.05.012}
+}
diff --git a/docs/visualization/visualize_2p_VR_behavior.ipynb b/docs/visualization/visualize_2p_VR_behavior.ipynb
diff --git a/requirements.txt b/requirements.txt
@@ -24,3 +24,4 @@ statsmodels==0.14.0
 suite2p==0.12.1
 tensortools==0.4
 zarr==2.13.3
+ndx-harvey-swac @ git+https://github.com/sytseng/ndx-harvey-swac
diff --git a/setup.py b/setup.py
@@ -15,7 +15,7 @@
     long_description_content_type="text/markdown",
     long_description=readme,
     author="Carter Peene",
-    version="1.0.0",
+    version="1.1.0",
     author_email="[email protected]",
     url="https://github.com/AllenInstitute/openscope_databook",
     license=license,