Merge branch 'main' of https://github.com/datajoint-company/datajoint-docs

Author: dimitri-yatsenko

.codespellrc

@@ -1,4 +1,4 @@
 [codespell]
 skip = .git,*.pdf,*.svg
 #
-ignore-words-list = shepard
+ignore-words-list = shepard,nevers

.cspell.json

@@ -191,6 +191,7 @@
         "Mobarhan",
         "Moser",
         "München",
+        "Nevers",
         "Neuro",
         "neuroanatomical",
         "Neurodata",

src/about/datajoint-team.md

@@ -6,17 +6,14 @@ as Principal Investigator.
 ## Scientists
 
 - Dimitri Yatsenko - PI
-- Kabilar Gunalan - Project Manager, Data Scientist
 - Thinh Nguyen - Data Scientist
-- Sid Hulyalkar - Data Scientist
-- Jaerong Ahn - Data Scientist
 - Kushal Bakshi - Data Scientist
+- Milagros Marín - Data Scientist
 
 ## Engineers
 
 - Drew Yang - Data Systems Engineer
-- Jeroen Verswijver - Software Engineer
-- Adib Baji - Software Engineer
+- Ethan Ho - Software Engineer
 
 ## Past contributors
 
@@ -37,6 +34,11 @@ as Principal Investigator.
 - Timothy Chandler - Data Systems Engineer
 - David Godinez - Data Engineer
 - Geetika Singh - Data Engineer
+- Kabilar Gunalan - Project Manager, Data Scientist
+- Jaerong Ahn - Data Scientist
+- Jeroen Verswijver - Software Engineer
+- Adib Baji - Software Engineer
+- Sid Hulyalkar - Data Scientist
 
 The first-person pronouns "we" and "our" in these documents refer to those listed above.
 

src/elements/index.md

@@ -79,6 +79,17 @@ Below are the projects that make up the family of open-source DataJoint Elements
 
     [:octicons-arrow-right-24: Docs](./element-deeplabcut/)
 
+-   :fontawesome-brands-python:{ .lg .middle } **Element MoSeq**
+
+    ---
+
+    A data pipeline for motion sequencing with Keypoint-MoSeq.
+
+    [:octicons-arrow-right-24: Interactive tutorial on GitHub
+    Codespaces](https://github.com/datajoint/element-moseq#interactive-tutorial){:target="_blank"}
+
+    [:octicons-arrow-right-24: Docs](./element-moseq/)
+
 -   :fontawesome-brands-python:{ .lg .middle } **Element Facemap**
 
     ---

src/partnerships/dandi.md

@@ -62,7 +62,7 @@ To achieve the aims of coordinated development, both projects appoint a primary
 contact (POC) to respond to questions relating to the integration and interoperability 
 of DataJoint Elements and DANDI.
 
-For 2022, the DataJoint Elements POC is Dr. Kabilar Gunalan (kabilar@datajoint.com)
+For 2022, the DataJoint Elements POC is Dr. Kushal Bakshi (kushal@datajoint.com)
 
 For 2022, the DANDI POC is Dr.Satrajit Ghosh ([email protected])
 

src/partnerships/facemap.md

@@ -60,7 +60,7 @@ To achieve the aims of coordinated development, both projects appoint a primary
 contact (POC) to respond to questions relating to the integration and interoperability 
 of DataJoint Elements and Facemap.
 
-For 2022, the DataJoint Elements POC is Dr. Kabilar Gunalan (kabilar@datajoint.com)
+For 2022, the DataJoint Elements POC is Dr. Kushal Bakshi (kushal@datajoint.com)
 
 For 2022, the Facemap POC is Dr. Carsen Stringer ([email protected])
 

src/partnerships/incf.md

@@ -1,3 +1,3 @@
 # INCF
 
-DataJoint is a [company member of INCF](https://www.incf.org/network/companies).
+DataJoint is a [company member of the INCF](https://www.incf.org/network/companies).

src/partnerships/nwb.md

@@ -62,7 +62,7 @@ To achieve the aims of coordinated development, both projects appoint a primary
 contact (POC) to respond to questions relating to the integration and interoperability
 of DataJoint Elements and NWB.
 
-For 2022, the DataJoint Elements POC is Dr. Kabilar Gunalan (kabilar@datajoint.com)
+For 2022, the DataJoint Elements POC is Dr. Kushal Bakshi (kushal@datajoint.com)
 
 For 2022, the NWB POC is Dr. Ryan Ly (Lawrence Berkeley National Laboratory)
 

src/partnerships/suite2p.md

@@ -60,7 +60,7 @@ To achieve the aims of coordinated development, both projects appoint a primary
 contact (POC) to respond to questions relating to the integration and interoperability 
 of DataJoint Elements and Suite2p.
 
-For 2022, the DataJoint Elements POC is Dr. Kabilar Gunalan (kabilar@datajoint.com)
+For 2022, the DataJoint Elements POC is Dr. Kushal Bakshi (kushal@datajoint.com)
 
 For 2022, the Suite2p POC is Dr. Carsen Stringer ([email protected])
 

src/projects/publications.md

@@ -4,7 +4,20 @@ Title: Publications
 <!-- markdownlint-disable MD013 -->
 
 The following publications relied on DataJoint open-source software for data analysis.  If your work uses DataJoint or DataJoint Elements, please cite the respective
-[manuscripts and RRIDs](./citation.md).
+[manuscripts and RRIDs](../about/citation.md).
+
+## 2024 
+
++ Kyu Hyun Lee, Eric L. Denovellis, Ryan Ly, Jeremy Magland, Jeff Soules, Alison E. Comrie, Daniel P. Gramling, Jennifer A. Guidera, Rhino Nevers, Philip Adenekan, Chris Brozdowski, Samuel R. Bray, Emily Monroe, Ji Hyun Bak, Michael E. Coulter, Xulu Sun, Emrey Broyles, Donghoon Shin, Sharon Chiang, Cristofer Holobetz, Andrew Tritt, Oliver Rübel, Thinh Nguyen, Dimitri Yatsenko, Joshua Chu, Caleb Kemere, Samuel Garcia, Alessio Buccino, Loren M. Frank
+[Spyglass: a framework for reproducible and shareable neuroscience research](https://doi.org/10.1101/2024.01.25.577295)
+*bioRxiv* 2024.01.25.577295
+
++ Gonzalo Cogno, S., Obenhaus, H. A., Lautrup, A., Jacobsen, R. I., Clopath, C., Andersson, S. O., ... & Moser, E. I. (2024). [Minute-scale oscillatory sequences in medial entorhinal cortex](https://www.nature.com/articles/s41586-023-06864-1). *Nature*, 625(7994), 338-344.
+
++ Cimorelli, A., Patel, A., Karakostas, T., & Cotton, R. J. (2024). [Validation of portable in-clinic video-based gait analysis for prosthesis users](https://www.nature.com/articles/s41598-024-53217-7). *Nature Scientific Reports*, 14(1), 3840.
+
++ Papadopouli, M., Koniotakis, E., Smyrnakis, I., Savaglio, M. A., Psilou, E., Brozi, C., ... & Smirnakis, S. M. (2024). [Brain orchestra under spontaneous conditions: Identifying communication modules from the functional architecture of area V1](https://doi.org/10.1101/2024.02.29.582364). *bioRxiv*, 2024-02.
+
 
 ## 2023 <!-- 5 -->
 
@@ -44,6 +57,8 @@ connectomics.](https://doi.org/10.1101/2023.03.14.532674){:target="_blank"}. *bi
 
 + Fu, J., Willeke, K. F., Pierzchlewicz, P. A., Muhammad, T., Denfield, G. H., Sinz, F. H., & Tolias, A. S. (2022). [Heterogeneous Orientation Tuning Across Sub-Regions of Receptive Fields of V1 Neurons in Mice](https://dx.doi.org/10.2139/ssrn.4029075){:target="_blank"}. *Available at SSRN 4029075*.
 
++ Zong, W., Obenhaus, H.A., Skytøen, E.R., Eneqvist, H., de Jong, N.L., Vale, R., Jorge, M.R., Moser, M.B. and Moser, E.I., 2022. [Large-scale two-photon calcium imaging in freely moving mice](https://www.sciencedirect.com/science/article/pii/S0092867422001970)(:target="_blank"}. *Cell*, 185(7), pp.1240-1256.
+
 + Goetz, J., Jessen, Z. F., Jacobi, A., Mani, A., Cooler, S., Greer, D., ... & Schwartz, G. W. (2022). [Unified classification of mouse retinal ganglion cells using function, morphology, and gene expression](https://doi.org/10.1016/j.celrep.2022.111040){:target="_blank"}. *Cell reports*, 40(2), 111040.
 
 + Huang, J. Y., Hess, M., Bajpai, A., Barton, S. J., Li, X., Hobson, L. N., & Lu, H. C.
@@ -80,6 +95,8 @@ connectomics.](https://doi.org/10.1101/2023.03.14.532674){:target="_blank"}. *bi
 
 + Cohrs, K.H. (2021). [Investigation of feedback mechanisms in visual cortex using deep learning models](http://dx.doi.org/10.13140/RG.2.2.35328.35845){:target="_blank"}. Master’s thesis. University of Göttingen.
 
++ Dennis, E. J., El Hady, A., Michaiel, A., Clemens, A., Tervo, D. R. G., Voigts, J., & Datta, S. R. (2021). [Systems neuroscience of natural behaviors in rodents](https://www.jneurosci.org/content/41/5/911.abstract). *Journal of Neuroscience*, 41(5), 911-919.
+
 + Finkelstein, A., Fontolan, L., Economo, M. N., Li, N., Romani, S., & Svoboda, K. (2021). [Attractor dynamics gate cortical information flow during decision-making](https://doi.org/10.1038/s41593-021-00840-6){:target="_blank"}. *Nature Neuroscience*. *24*(6), 843-850.
 
 + Franke, K., Willeke, K. F., Ponder, K., Galdamez, M., Muhammad, T., Patel, S., Froudarakis, E., Reimer, J., Sinz, F., & Tolias, A. (2021). [Behavioral state tunes mouse vision to ethological features through pupil dilation](https://doi.org/10.1101/2021.09.03.458870){:target="_blank"}. *bioRxiv*.