Merge remote-tracking branch 'refs/remotes/euler/master'

README.md

@@ -1,3 +1,26 @@
-# rave_data
+# Data: Removing Inter-Experimental Variability from Functional Data in Systems Neuroscience
+This repository hosts the data of [Gonschorek, Höfling et al. (2021), *Removing Inter-Experimental Variability from Functional Data in Systems Neuroscience*, NeurIPS 2021][1]. The corresponding code for the implementation can be found on [GitHub][2].
 
-Simulated and recorded responses of mouse retinal bipolar cells to the chirp stimulus
+The files contain the following data and information:
+
+* bio/bc_dataset_A (pickle):
+    * This file contains the preprocessed bipolar cell data in response to the local and full-field chirp, their IPL (inner plexiform layer) depths and cell type labels obtained from Franke, Berens et al. (2017), *Inhibition decorrelates visual feature representation in the inner retina*, Nature. This dataset is licensed under the [CC0 1.0 Universal (CC0 1.0) Public Domain Dedication][3] and can be downloaded in full (incl. raw data) at [datadryad][4]
+
+* bio/bc_dataset_B (pickle)
+    * This file contains the preprocessed bipolar cell data in response to the local and full-field chirp and their IPL depths obtained from Zhao, Klindt et al. (2020), *The temporal structure of the inner retina at a single glance*, Scientific Reports. 
+
+* ipl/BC_Profiles_Helmstaedter (txt)
+    * This file contains electron-microscopy (EM) data of axonal stratification profiles of bipolar cell types.
+    * array of shape 400x14, array[d, t] = p(IPL depth = d|BC type = t)
+
+* ipl/ipl (mat)
+    * Matlab file containing a dictionary with keys "d" and "prior"; d: 400x1 array, IPL depth samples; prior: 400 x 14 array, with array[d, t] = p(BC type = t|IPL depth = d).
+
+* silico/sim_dataset (pickle)
+    * This file contains the dataset object of bipolar cell responses to the chirp stimulus simulated using the model described in [Schröder, Klindt et al. (2020), *System Identification with Biophysical Constraints: A Circuit Model of the Inner Retina*, NeurIPS 2020][5].
+ 
+[1]: https://www.biorxiv.org/content/10.1101/2021.10.29.466492v2 "Gonschorek, Höfling et al. (2021)" 
+[2]: https://github.com/eulerlab/rave "rave"
+[3]: https://creativecommons.org/publicdomain/zero/1.0/ "CC0 1.0 Universal (CC0 1.0) Public Domain Dedication"
+[4]: https://datadryad.org/stash/dataset/doi:10.5061/dryad.rs2qp "datadryad"
+[5]: https://proceedings.neurips.cc/paper/2020/file/b139e104214a08ae3f2ebcce149cdf6e-Paper.pdf "Schröder, Klindt et al. (2020)"

datacite.yml

@@ -19,6 +19,10 @@ authors:
     firstname: Timm
     lastname: Schubert
     affiliation: 'University of Tübingen'
+  - 
+    firstname: Benjamin
+    lastname: Dunn
+    affiliation: 'Norwegian University of Science and Technology'
   -
     firstname: Philipp
     lastname: Berens
@@ -34,9 +38,11 @@ authors:
 title: ' Simulated and recorded responses of mouse retinal bipolar cells to the chirp stimulus '
 description: " Simulated and recorded responses of \n mouse retinal bipolar cells to the chirp stimulus \n"
 keywords:
-  - Neuroscience
+  - neuroscience
   - retina
   - bipolar cells
+  - two-photon microscopy
+  - synthetic data
   - inter-experimental variability
 license:
   name: 'Creative Commons CC BY-NC-SA'
@@ -45,7 +51,7 @@ references:
   -
     id: "doi:10.1101/2021.10.29.466492 "
     reftype: "IsSupplementTo"
-    citation: "Removing Inter-Experimental Variability from Functional Data in Systems Neuroscience \n Dominic Gonschorek, Larissa Hoefling, Klaudia P Szatko, Katrin Franke, Timm Schubert, Benjamin Dunn, Philipp Berens, David A Klindt, Thomas Euler \n bioRxiv 2021.10.29.466492; doi: https://doi.org/10.1101/2021.10.29.466492 "
+    citation: "Removing Inter-Experimental Variability from Functional Data in Systems Neuroscience (2021) Dominic Gonschorek, Larissa Hoefling, Klaudia P Szatko, Katrin Franke, Timm Schubert, Benjamin Dunn, Philipp Berens, David A Klindt, Thomas Euler bioRxiv 2021.10.29.466492; doi: https://doi.org/10.1101/2021.10.29.466492 "
   - 
     id: "10.1038/nature21394"
     reftype: "IsSupplementTo"
@@ -54,9 +60,20 @@ references:
     id: "10.1038/s41598-020-60214-z"
     reftype: "IsSupplementTo"
     citation: "Zhao, Z., Klindt, D. A., Maia Chagas, A., Szatko, K. P., Rogerson, L., Protti, D. A., … Euler, T. (2020). The temporal structure of the inner retina at a single glance. Scientific Reports, 10(1), 4399. https://doi.org/10.1038/s41598-020-60214-z"
+  -
+    id: "10.1038/nature12346"
+    reftype: "IsDescribedBy"
+    citation: "Helmstaedter, M., Briggman, K. L., Turaga, S. C., Jain, V., Seung, H. S., & Denk, W. (2013). Connectomic reconstruction of the inner plexiform layer in the mouse retina. Nature, 500(7461), 168–174. https://doi.org/10.1038/nature12346"
+  -
+    id: "10.7554/eLife.20041"
+    reftype: "IsDescribedBy"
+    citation: "Behrens, C., Schubert, T., Haverkamp, S., Euler, T., & Berens, P. (2016). Connectivity map of bipolar cells and photoreceptors in the mouse retina. ELife, 5(NOVEMBER2016), 1–20. https://doi.org/10.7554/eLife.20041"
+
 funding:
   - 'DFG, 335549539/GRK2381'
   - 'DFG, 276693517/CRC1233'
+  - 'DFG, Machine Learning Cluster of Excellence, EXC number 2064/1 - Project #390727645'
+  - 'BMBF, Tübingen AI Center, FKZ: 01IS18039A'
   - 'Research Council of Norway, 90532703/FRIPRO'
 resourcetype: Dataset
 templateversion: 1.2