[Feature] Merging "Total spiking probability edges" into elephant (Ne…

…uralEnsemble#560) * Feat: Add basic scaffold for total_spiking_probability_edges * Feat: Add filterpair generation * Feat: Add normalized_cross_correlation * Feat: Add total_spiking_probability_edges * Refactor: Rename filter parameters * Feat: Add function to compute connectivity_matrix * Feat: Combine total_spiking_probability_edges and get_connectivty_matrix * Docs: Explenation why mean values are ommited in NCC * Refactor: Naming conventions * Fix: Extra dimension on delay_matrix * Test: Add test for total_spiking_probability_edges * Fix: Incorrect repo path * Fix Incorrect repo path part 2 * Docs: Add further documentation * docs: Fix typos Co-authored-by: Moritz Kern <[email protected]> * fixed pep8 issue in total_spiking_probability_edges.py * fixed pep8 issue in test_total_spiking_probability_edges.py * convert tests to unittest.TestCase classes * add zenodo info --------- Co-authored-by: Moritz Kern <[email protected]> Co-authored-by: Moritz-Alexander-Kern <[email protected]>
INM-6 · Mar 25, 2024 · 6363690 · 6363690
1 parent d046165
commit 6363690
Show file tree

Hide file tree

Showing 8 changed files with 624 additions and 0 deletions.
diff --git a/.zenodo.json b/.zenodo.json
@@ -9,6 +9,11 @@
             "orcid": "0000-0001-7292-1982",
             "affiliation": "Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA-Institute Brain Structure-Function Relationships (INM-10), Jülich Research Centre, Jülich, Germany",
             "name": "Kern, Moritz"
+        },
+        {
+            "orcid": "0009-0003-9352-9826",
+            "affiliation": "BioMEMS Lab, University of Applied Sciences Aschaffenburg, Germany",
+            "name": "Richter, Felician"
         }
     ],
 

diff --git a/doc/authors.rst b/doc/authors.rst
@@ -51,6 +51,7 @@ contribution, and may not be the current affiliation of a contributor.
 * Florian Porrmann [13]
 * Sarah Pilz [13]
 * Oliver Kloß [1]
+* Felician Richter [12]
 
 1. Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA-Institute Brain Structure-Function Relationships (INM-10), Jülich Research Centre, Jülich, Germany
 2. Unité de Neurosciences, Information et Complexité, CNRS UPR 3293, Gif-sur-Yvette, France

diff --git a/doc/bib/elephant.bib b/doc/bib/elephant.bib
@@ -466,3 +466,17 @@ @article{Deger12_443
 	title = {Statistical properties of superimposed stationary spike trains},
 	volume = 32,
 	year = 2012}
+
+
+@article{de_blasi19_169,
+	title = {Total spiking probability edges: {A} cross-correlation based method for effective connectivity estimation of cortical spiking neurons},
+	volume = {312},
+	shorttitle = {Total spiking probability edges},
+	doi = {10.1016/j.jneumeth.2018.11.013},
+	language = {en},
+	journal = {Journal of Neuroscience Methods},
+	author = {{De Blasi}, Stefano and Ciba, Manuel and Bahmer, Andreas and Thielemann, Christiane},
+	month = jan,
+	year = {2019},
+	pages = {169--181},
+}
diff --git a/doc/modules.rst b/doc/modules.rst
@@ -32,11 +32,17 @@ Spike trains
     reference/_spike_train_processing
     reference/_spike_train_patterns
 
+.. toctree::
+    :maxdepth: 1
+
+    reference/functional_connectivity_estimation.rst
+
 .. toctree::
     :maxdepth: 1
 
     reference/change_point_detection
     reference/gpfa
+
 .. toctree::
     :maxdepth: 1
 

diff --git a/doc/reference/functional_connectivity_estimation.rst b/doc/reference/functional_connectivity_estimation.rst
@@ -0,0 +1,5 @@
+==================================
+Functional connectivity estimation
+==================================
+
+.. automodule:: elephant.functional_connectivity
diff --git a/elephant/functional_connectivity.py b/elephant/functional_connectivity.py
@@ -0,0 +1,31 @@
+"""
+Functions for analysing and estimating firing-patterns and connectivity among neurons
+in order to better understand the underlying neural-networks and information-flow
+between neurons.
+
+
+Network connectivity estimation
+*******************************
+
+.. autosummary::
+    :toctree: _toctree/functional_connectivity/
+
+    total_spiking_probability_edges
+
+References
+----------
+
+.. bibliography::
+   :keyprefix: functional_connectivity-
+
+
+:copyright: Copyright 2014-2023 by the Elephant team, see `doc/authors.rst`.
+:license: Modified BSD, see LICENSE.txt for details.
+"""
+
+from elephant.functional_connectivity_src.total_spiking_probability_edges import (
+    total_spiking_probability_edges,
+)
+
+__all__ = ["total_spiking_probability_edges"]
+