diff --git a/CITATION b/CITATION
index 5bbbc251301dd686a17080f842c7dd779adae4c4..89bd8489e45e1576db9690fc803b09cb05ed0c15 100644
--- a/CITATION
+++ b/CITATION
@@ -1,6 +1,6 @@
@article{Schuecker17,
author = {Schuecker, Jannis and Schmidt, Maximilian and van Albada, Sacha J. and Diesmann, Markus and Helias, Moritz},
- journal = ploscb,
+ journal = {PLOS Computational Biology},
publisher = {Public Library of Science},
title = {Fundamental Activity Constraints Lead to Specific Interpretations of the Connectome},
year = {2017},
@@ -8,18 +8,21 @@
volume = {13},
pages = {1-25},
number = {2},
- doi = {10.1371/journal.pcbi.1005179}
+ doi = {10.1371/jour.pcbi.1005179}
}
-@article{Schmidt17,
- title={Multi-scale account of the network structure of macaque visual cortex},
- author={Schmidt, Maximilian and Bakker, Rembrandt and Hilgetag, Claus Christian and Diesmann, Markus and van Albada, Sacha Jennifer},
- journal=bsf,
- year={2017},
- doi={https://doi.org/10.1007/s00429-017-1554-4}
+@article{Schmidt18_1,
+ title={Multi-scale account of the network structure of macaque visual cortex},
+ author={Schmidt, Maximilian and Bakker, Rembrandt and Hilgetag, Claus Christian and Diesmann, Markus and van Albada, Sacha Jennifer},
+ journal={Brain Structure and Function},
+ year={2018},
+ volume={223},
+ number={3},
+ pages={1409--1435},
+ doi={https://doi.org/10.1007/s00429-017-1554-4}
}
-@article{Schmidt18,
+@article{Schmidt18_2,
title={A multi-scale layer-resolved spiking network model of resting-state dynamics in macaque visual cortical areas}
author={Schmidt, Maximilian and Bakker, Rembrandt and Shen, Kelly and Bezgin, Gleb and Diesmann, Markus and Sacha Jennifer van Albada},
year={2018},
diff --git a/README.md b/README.md
index 89bf81257e27d7a88776a3f542ff2a0707f065af..9fb12196be94872c37d9e612e6194e3eb1b83882 100644
--- a/README.md
+++ b/README.md
@@ -5,9 +5,9 @@ This code implements the spiking network model of macaque visual cortex develope
at the Institute of Neuroscience and Medicine (INM-6), Research Center Jülich.
The model has been documented in the following publications:
-1. Schmidt M, Bakker R, Hilgetag CC, Diesmann M & van Albada SJ (2017)
+1. Schmidt M, Bakker R, Hilgetag CC, Diesmann M & van Albada SJ
Multi-scale account of the network structure of macaque visual cortex
- Brain Structure and Function (2017) [https://doi.org/10.1007/s00429-017-1554-4](https://doi.org/10.1007/s00429-017-1554-4)
+ Brain Structure and Function (2018), 223:1409 [https://doi.org/10.1007/s00429-017-1554-4](https://doi.org/10.1007/s00429-017-1554-4)
2. Schuecker J, Schmidt M, van Albada SJ, Diesmann M & Helias M (2017)
Fundamental Activity Constraints Lead to Specific Interpretations of the Connectome.
@@ -84,7 +84,7 @@ the figures from [1]. The scripts for [2] and [3] will follow soon.
If snakemake is installed, the figures can be produced by executing
`snakemake` in the respective folder:
- cd figures/Schmidt2017/
+ cd figures/Schmidt2018/
snakemake
@@ -181,11 +181,11 @@ Note that NEST needs to be installed separately, see <http://www.nest-simulator.
In addition, reproducing the figures of [1] requires networkx, python-igraph and pyx. To install these additional packages, execute:
-`pip install -r figures/Schmidt2017/additional_requirements.txt`
+`pip install -r figures/Schmidt2018/additional_requirements.txt`
In addition, Figure 7 of [1] requires installing the `infomap` package to perform the map equation clustering. See <http://www.mapequation.org/code.html> for all necessary information.
-The SLN fit in `multiarea_model/data_multiarea/VisualCortex_Data.py` and `figures/Schmidt2017/Fig5_cc_laminar_pattern.py` requires an installation of R and the R library `aod` (<http://cran.r-project.org/package=aod>). Without R installation, both scripts will directly use the resulting values of the fit (see Fig. 5 of [1]).
+The SLN fit in `multiarea_model/data_multiarea/VisualCortex_Data.py` and `figures/Schmidt2018/Fig5_cc_laminar_pattern.py` requires an installation of R and the R library `aod` (<http://cran.r-project.org/package=aod>). Without R installation, both scripts will directly use the resulting values of the fit (see Fig. 5 of [1]).
## Contributors
diff --git a/figures/Schmidt2017/cmap.py b/figures/Schmidt2017/cmap.py
deleted file mode 100644
index 62d9c23c629f63cbc96592f4b63a6bde90494973..0000000000000000000000000000000000000000
--- a/figures/Schmidt2017/cmap.py
+++ /dev/null
@@ -1,263 +0,0 @@
-from matplotlib.colors import LinearSegmentedColormap
-"""
-Manual implementation of the inferno colormap
-which is part of matplotlib since version 1.5
-"""
-cm_data = [[1.46159096e-03, 4.66127766e-04, 1.38655200e-02],
- [2.26726368e-03, 1.26992553e-03, 1.85703520e-02],
- [3.29899092e-03, 2.24934863e-03, 2.42390508e-02],
- [4.54690615e-03, 3.39180156e-03, 3.09092475e-02],
- [6.00552565e-03, 4.69194561e-03, 3.85578980e-02],
- [7.67578856e-03, 6.13611626e-03, 4.68360336e-02],
- [9.56051094e-03, 7.71344131e-03, 5.51430756e-02],
- [1.16634769e-02, 9.41675403e-03, 6.34598080e-02],
- [1.39950388e-02, 1.12247138e-02, 7.18616890e-02],
- [1.65605595e-02, 1.31362262e-02, 8.02817951e-02],
- [1.93732295e-02, 1.51325789e-02, 8.87668094e-02],
- [2.24468865e-02, 1.71991484e-02, 9.73274383e-02],
- [2.57927373e-02, 1.93306298e-02, 1.05929835e-01],
- [2.94324251e-02, 2.15030771e-02, 1.14621328e-01],
- [3.33852235e-02, 2.37024271e-02, 1.23397286e-01],
- [3.76684211e-02, 2.59207864e-02, 1.32232108e-01],
- [4.22525554e-02, 2.81385015e-02, 1.41140519e-01],
- [4.69146287e-02, 3.03236129e-02, 1.50163867e-01],
- [5.16437624e-02, 3.24736172e-02, 1.59254277e-01],
- [5.64491009e-02, 3.45691867e-02, 1.68413539e-01],
- [6.13397200e-02, 3.65900213e-02, 1.77642172e-01],
- [6.63312620e-02, 3.85036268e-02, 1.86961588e-01],
- [7.14289181e-02, 4.02939095e-02, 1.96353558e-01],
- [7.66367560e-02, 4.19053329e-02, 2.05798788e-01],
- [8.19620773e-02, 4.33278666e-02, 2.15289113e-01],
- [8.74113897e-02, 4.45561662e-02, 2.24813479e-01],
- [9.29901526e-02, 4.55829503e-02, 2.34357604e-01],
- [9.87024972e-02, 4.64018731e-02, 2.43903700e-01],
- [1.04550936e-01, 4.70080541e-02, 2.53430300e-01],
- [1.10536084e-01, 4.73986708e-02, 2.62912235e-01],
- [1.16656423e-01, 4.75735920e-02, 2.72320803e-01],
- [1.22908126e-01, 4.75360183e-02, 2.81624170e-01],
- [1.29284984e-01, 4.72930838e-02, 2.90788012e-01],
- [1.35778450e-01, 4.68563678e-02, 2.99776404e-01],
- [1.42377819e-01, 4.62422566e-02, 3.08552910e-01],
- [1.49072957e-01, 4.54676444e-02, 3.17085139e-01],
- [1.55849711e-01, 4.45588056e-02, 3.25338414e-01],
- [1.62688939e-01, 4.35542881e-02, 3.33276678e-01],
- [1.69575148e-01, 4.24893149e-02, 3.40874188e-01],
- [1.76493202e-01, 4.14017089e-02, 3.48110606e-01],
- [1.83428775e-01, 4.03288858e-02, 3.54971391e-01],
- [1.90367453e-01, 3.93088888e-02, 3.61446945e-01],
- [1.97297425e-01, 3.84001825e-02, 3.67534629e-01],
- [2.04209298e-01, 3.76322609e-02, 3.73237557e-01],
- [2.11095463e-01, 3.70296488e-02, 3.78563264e-01],
- [2.17948648e-01, 3.66146049e-02, 3.83522415e-01],
- [2.24762908e-01, 3.64049901e-02, 3.88128944e-01],
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- [9.86502013e-01, 6.23104667e-01, 2.78139496e-02],
- [9.86963670e-01, 6.30485011e-01, 3.09075459e-02],
- [9.87337182e-01, 6.37890424e-01, 3.49160639e-02],
- [9.87622296e-01, 6.45320152e-01, 3.98857472e-02],
- [9.87818759e-01, 6.52773439e-01, 4.55808037e-02],
- [9.87926330e-01, 6.60249526e-01, 5.17503867e-02],
- [9.87944783e-01, 6.67747641e-01, 5.83286889e-02],
- [9.87873910e-01, 6.75267000e-01, 6.52570167e-02],
- [9.87713535e-01, 6.82806802e-01, 7.24892330e-02],
- [9.87463516e-01, 6.90366218e-01, 7.99897176e-02],
- [9.87123759e-01, 6.97944391e-01, 8.77314215e-02],
- [9.86694229e-01, 7.05540424e-01, 9.56941797e-02],
- [9.86174970e-01, 7.13153375e-01, 1.03863324e-01],
- [9.85565739e-01, 7.20782460e-01, 1.12228756e-01],
- [9.84865203e-01, 7.28427497e-01, 1.20784651e-01],
- [9.84075129e-01, 7.36086521e-01, 1.29526579e-01],
- [9.83195992e-01, 7.43758326e-01, 1.38453063e-01],
- [9.82228463e-01, 7.51441596e-01, 1.47564573e-01],
- [9.81173457e-01, 7.59134892e-01, 1.56863224e-01],
- [9.80032178e-01, 7.66836624e-01, 1.66352544e-01],
- [9.78806183e-01, 7.74545028e-01, 1.76037298e-01],
- [9.77497453e-01, 7.82258138e-01, 1.85923357e-01],
- [9.76108474e-01, 7.89973753e-01, 1.96017589e-01],
- [9.74637842e-01, 7.97691563e-01, 2.06331925e-01],
- [9.73087939e-01, 8.05409333e-01, 2.16876839e-01],
- [9.71467822e-01, 8.13121725e-01, 2.27658046e-01],
- [9.69783146e-01, 8.20825143e-01, 2.38685942e-01],
- [9.68040817e-01, 8.28515491e-01, 2.49971582e-01],
- [9.66242589e-01, 8.36190976e-01, 2.61533898e-01],
- [9.64393924e-01, 8.43848069e-01, 2.73391112e-01],
- [9.62516656e-01, 8.51476340e-01, 2.85545675e-01],
- [9.60625545e-01, 8.59068716e-01, 2.98010219e-01],
- [9.58720088e-01, 8.66624355e-01, 3.10820466e-01],
- [9.56834075e-01, 8.74128569e-01, 3.23973947e-01],
- [9.54997177e-01, 8.81568926e-01, 3.37475479e-01],
- [9.53215092e-01, 8.88942277e-01, 3.51368713e-01],
- [9.51546225e-01, 8.96225909e-01, 3.65627005e-01],
- [9.50018481e-01, 9.03409063e-01, 3.80271225e-01],
- [9.48683391e-01, 9.10472964e-01, 3.95289169e-01],
- [9.47594362e-01, 9.17399053e-01, 4.10665194e-01],
- [9.46809163e-01, 9.24168246e-01, 4.26373236e-01],
- [9.46391536e-01, 9.30760752e-01, 4.42367495e-01],
- [9.46402951e-01, 9.37158971e-01, 4.58591507e-01],
- [9.46902568e-01, 9.43347775e-01, 4.74969778e-01],
- [9.47936825e-01, 9.49317522e-01, 4.91426053e-01],
- [9.49544830e-01, 9.55062900e-01, 5.07859649e-01],
- [9.51740304e-01, 9.60586693e-01, 5.24203026e-01],
- [9.54529281e-01, 9.65895868e-01, 5.40360752e-01],
- [9.57896053e-01, 9.71003330e-01, 5.56275090e-01],
- [9.61812020e-01, 9.75924241e-01, 5.71925382e-01],
- [9.66248822e-01, 9.80678193e-01, 5.87205773e-01],
- [9.71161622e-01, 9.85282161e-01, 6.02154330e-01],
- [9.76510983e-01, 9.89753437e-01, 6.16760413e-01],
- [9.82257307e-01, 9.94108844e-01, 6.31017009e-01],
- [9.88362068e-01, 9.98364143e-01, 6.44924005e-01]]
-
-cm_inferno = LinearSegmentedColormap.from_list(__file__, cm_data)
diff --git a/figures/Schmidt2017/Fig1_model_overview.eps b/figures/Schmidt2018/Fig1_model_overview.eps
similarity index 100%
rename from figures/Schmidt2017/Fig1_model_overview.eps
rename to figures/Schmidt2018/Fig1_model_overview.eps
diff --git a/figures/Schmidt2017/Fig2_anatomy.eps b/figures/Schmidt2018/Fig2_anatomy.eps
similarity index 100%
rename from figures/Schmidt2017/Fig2_anatomy.eps
rename to figures/Schmidt2018/Fig2_anatomy.eps
diff --git a/figures/Schmidt2017/Fig2_anatomy.py b/figures/Schmidt2018/Fig2_anatomy.py
similarity index 100%
rename from figures/Schmidt2017/Fig2_anatomy.py
rename to figures/Schmidt2018/Fig2_anatomy.py
diff --git a/figures/Schmidt2017/Fig3_construction.py b/figures/Schmidt2018/Fig3_construction.py
similarity index 100%
rename from figures/Schmidt2017/Fig3_construction.py
rename to figures/Schmidt2018/Fig3_construction.py
diff --git a/figures/Schmidt2017/Fig3_syntypes.eps b/figures/Schmidt2018/Fig3_syntypes.eps
similarity index 100%
rename from figures/Schmidt2017/Fig3_syntypes.eps
rename to figures/Schmidt2018/Fig3_syntypes.eps
diff --git a/figures/Schmidt2017/Fig4_connectivity.eps b/figures/Schmidt2018/Fig4_connectivity.eps
similarity index 100%
rename from figures/Schmidt2017/Fig4_connectivity.eps
rename to figures/Schmidt2018/Fig4_connectivity.eps
diff --git a/figures/Schmidt2017/Fig4_connectivity.py b/figures/Schmidt2018/Fig4_connectivity.py
similarity index 100%
rename from figures/Schmidt2017/Fig4_connectivity.py
rename to figures/Schmidt2018/Fig4_connectivity.py
diff --git a/figures/Schmidt2017/Fig5_cc_laminar_pattern.eps b/figures/Schmidt2018/Fig5_cc_laminar_pattern.eps
similarity index 100%
rename from figures/Schmidt2017/Fig5_cc_laminar_pattern.eps
rename to figures/Schmidt2018/Fig5_cc_laminar_pattern.eps
diff --git a/figures/Schmidt2017/Fig5_cc_laminar_pattern.py b/figures/Schmidt2018/Fig5_cc_laminar_pattern.py
similarity index 100%
rename from figures/Schmidt2017/Fig5_cc_laminar_pattern.py
rename to figures/Schmidt2018/Fig5_cc_laminar_pattern.py
diff --git a/figures/Schmidt2017/Fig5_syn_illustration.eps b/figures/Schmidt2018/Fig5_syn_illustration.eps
similarity index 100%
rename from figures/Schmidt2017/Fig5_syn_illustration.eps
rename to figures/Schmidt2018/Fig5_syn_illustration.eps
diff --git a/figures/Schmidt2017/Fig6_conn_indegree.eps b/figures/Schmidt2018/Fig6_conn_indegree.eps
similarity index 100%
rename from figures/Schmidt2017/Fig6_conn_indegree.eps
rename to figures/Schmidt2018/Fig6_conn_indegree.eps
diff --git a/figures/Schmidt2017/Fig6_conn_prob.eps b/figures/Schmidt2018/Fig6_conn_prob.eps
similarity index 100%
rename from figures/Schmidt2017/Fig6_conn_prob.eps
rename to figures/Schmidt2018/Fig6_conn_prob.eps
diff --git a/figures/Schmidt2017/Fig6_connectivity_measures.eps b/figures/Schmidt2018/Fig6_connectivity_measures.eps
similarity index 100%
rename from figures/Schmidt2017/Fig6_connectivity_measures.eps
rename to figures/Schmidt2018/Fig6_connectivity_measures.eps
diff --git a/figures/Schmidt2017/Fig6_connectivity_measures.py b/figures/Schmidt2018/Fig6_connectivity_measures.py
similarity index 100%
rename from figures/Schmidt2017/Fig6_connectivity_measures.py
rename to figures/Schmidt2018/Fig6_connectivity_measures.py
diff --git a/figures/Schmidt2017/Fig7_community_structure.eps b/figures/Schmidt2018/Fig7_community_structure.eps
similarity index 100%
rename from figures/Schmidt2017/Fig7_community_structure.eps
rename to figures/Schmidt2018/Fig7_community_structure.eps
diff --git a/figures/Schmidt2017/Fig7_community_structure.py b/figures/Schmidt2018/Fig7_community_structure.py
similarity index 100%
rename from figures/Schmidt2017/Fig7_community_structure.py
rename to figures/Schmidt2018/Fig7_community_structure.py
diff --git a/figures/Schmidt2017/Fig8_laminar_paths.eps b/figures/Schmidt2018/Fig8_laminar_paths.eps
similarity index 100%
rename from figures/Schmidt2017/Fig8_laminar_paths.eps
rename to figures/Schmidt2018/Fig8_laminar_paths.eps
diff --git a/figures/Schmidt2017/Fig8_laminar_paths.py b/figures/Schmidt2018/Fig8_laminar_paths.py
similarity index 100%
rename from figures/Schmidt2017/Fig8_laminar_paths.py
rename to figures/Schmidt2018/Fig8_laminar_paths.py
diff --git a/figures/Schmidt2017/README.md b/figures/Schmidt2018/README.md
similarity index 90%
rename from figures/Schmidt2017/README.md
rename to figures/Schmidt2018/README.md
index 0076ca9a7fdd5aa61f017cbc52f6a2abc1438a82..9a8558fea1619b7c34fa26f2e88b99d8fa38bf3c 100644
--- a/figures/Schmidt2017/README.md
+++ b/figures/Schmidt2018/README.md
@@ -1,6 +1,6 @@
## Figures of Schmidt M, Bakker R, Hilgetag C-C, Diesmann M and van Albada SJ: "Multi-scale account of the network structure of macaque visual cortex"
-This folder contains the scripts to reproduce all figures of Schmidt M, Bakker R, Hilgetag C-C, Diesmann M and van Albada SJ: "Multi-scale account of the network structure of macaque visual cortex", Brain Structure and Function (2017) [https://doi.org/10.1007/s00429-017-1554-4](https://doi.org/10.1007/s00429-017-1554-4)
+This folder contains the scripts to reproduce all figures of Schmidt M, Bakker R, Hilgetag C-C, Diesmann M and van Albada SJ: "Multi-scale account of the network structure of macaque visual cortex", Brain Structure and Function (2018), 223:1409 [https://doi.org/10.1007/s00429-017-1554-4](https://doi.org/10.1007/s00429-017-1554-4)
Please note: Figures 2, 5, and 8 show slight deviations from the published figures in the paper. Published Figures 2 and 5 miss a few data points. This error slipped in during the review process. Importantly, the presented fits are identical in the (correct) figures in this repository and in the manuscript. These deviations thus do not affect the scientific conclusions.
diff --git a/figures/Schmidt2017/Snakefile b/figures/Schmidt2018/Snakefile
similarity index 100%
rename from figures/Schmidt2017/Snakefile
rename to figures/Schmidt2018/Snakefile
diff --git a/figures/Schmidt2017/additional_requirements.txt b/figures/Schmidt2018/additional_requirements.txt
similarity index 100%
rename from figures/Schmidt2017/additional_requirements.txt
rename to figures/Schmidt2018/additional_requirements.txt
diff --git a/figures/Schmidt2017/graph_helpers.py b/figures/Schmidt2018/graph_helpers.py
similarity index 99%
rename from figures/Schmidt2017/graph_helpers.py
rename to figures/Schmidt2018/graph_helpers.py
index 3e6ff8802d2b03721ca8660699db094609ebbb11..5047f8265b8140b504fd4ca37197ef9000c6a76f 100644
--- a/figures/Schmidt2017/graph_helpers.py
+++ b/figures/Schmidt2018/graph_helpers.py
@@ -101,7 +101,7 @@ def modularity(g, membership):
and cluster memberships.
See Schmidt, M., Bakker, R., Hilgetag, C.C. et al.
- Brain Structure and Function (2017),
+ Brain Structure and Function (2018), 223:1409,
for a derivation.
Parameters
@@ -138,7 +138,7 @@ def all_pairs_bellman_ford_path(g, weight='distance'):
Compute the shorted paths between nodes of a graph
using the Bellman-Ford algorithm.
See Schmidt, M., Bakker, R., Hilgetag, C.C. et al.
- Brain Structure and Function (2017),
+ Brain Structure and Function (2018), 223:1409,
for details.
Parameters
diff --git a/figures/Schmidt2017/helpers.py b/figures/Schmidt2018/helpers.py
similarity index 99%
rename from figures/Schmidt2017/helpers.py
rename to figures/Schmidt2018/helpers.py
index c716a177ceaf51e29bca5cffb3d0869bffa46aa6..53f46ec60684191eb99c3ca7ad6adcc1b3a8a7d1 100644
--- a/figures/Schmidt2017/helpers.py
+++ b/figures/Schmidt2018/helpers.py
@@ -61,7 +61,7 @@ def structural_gradient(target_area, source_area, structure):
"""
Returns the structural gradient between two areas
See Schmidt, M., Bakker, R., Hilgetag, C.C. et al.
- Brain Structure and Function (2017),
+ Brain Structure and Function (2018), 223:1409,
for a definition.
Parameters
diff --git a/figures/Schmidt2017/plotcolors.py b/figures/Schmidt2018/plotcolors.py
similarity index 100%
rename from figures/Schmidt2017/plotcolors.py
rename to figures/Schmidt2018/plotcolors.py
diff --git a/figures/Schmidt2017/plotfuncs.py b/figures/Schmidt2018/plotfuncs.py
similarity index 100%
rename from figures/Schmidt2017/plotfuncs.py
rename to figures/Schmidt2018/plotfuncs.py
diff --git a/figures/Schmidt2017/plotstyle.rc b/figures/Schmidt2018/plotstyle.rc
similarity index 100%
rename from figures/Schmidt2017/plotstyle.rc
rename to figures/Schmidt2018/plotstyle.rc
diff --git a/figures/Schmidt2017/tex/FB_paths.tex b/figures/Schmidt2018/tex/FB_paths.tex
similarity index 100%
rename from figures/Schmidt2017/tex/FB_paths.tex
rename to figures/Schmidt2018/tex/FB_paths.tex
diff --git a/figures/Schmidt2017/tex/FF_paths.tex b/figures/Schmidt2018/tex/FF_paths.tex
similarity index 100%
rename from figures/Schmidt2017/tex/FF_paths.tex
rename to figures/Schmidt2018/tex/FF_paths.tex
diff --git a/figures/Schmidt2017/tex/HL_paths.tex b/figures/Schmidt2018/tex/HL_paths.tex
similarity index 100%
rename from figures/Schmidt2017/tex/HL_paths.tex
rename to figures/Schmidt2018/tex/HL_paths.tex
diff --git a/figures/Schmidt2017/tex/HZ_paths.tex b/figures/Schmidt2018/tex/HZ_paths.tex
similarity index 100%
rename from figures/Schmidt2017/tex/HZ_paths.tex
rename to figures/Schmidt2018/tex/HZ_paths.tex
diff --git a/figures/Schmidt2017/tex/LH_paths.tex b/figures/Schmidt2018/tex/LH_paths.tex
similarity index 100%
rename from figures/Schmidt2017/tex/LH_paths.tex
rename to figures/Schmidt2018/tex/LH_paths.tex
diff --git a/figures/Schmidt2017/tex/compile_tex.sh b/figures/Schmidt2018/tex/compile_tex.sh
similarity index 100%
rename from figures/Schmidt2017/tex/compile_tex.sh
rename to figures/Schmidt2018/tex/compile_tex.sh
diff --git a/figures/Schmidt2017/tex/define_bools.tex b/figures/Schmidt2018/tex/define_bools.tex
similarity index 100%
rename from figures/Schmidt2017/tex/define_bools.tex
rename to figures/Schmidt2018/tex/define_bools.tex
diff --git a/figures/Schmidt2017/tex/defs.tex b/figures/Schmidt2018/tex/defs.tex
similarity index 100%
rename from figures/Schmidt2017/tex/defs.tex
rename to figures/Schmidt2018/tex/defs.tex
diff --git a/figures/Schmidt2017/tex/draw_paths.tex b/figures/Schmidt2018/tex/draw_paths.tex
similarity index 100%
rename from figures/Schmidt2017/tex/draw_paths.tex
rename to figures/Schmidt2018/tex/draw_paths.tex
diff --git a/figures/Schmidt2017/tex/draw_pops.tex b/figures/Schmidt2018/tex/draw_pops.tex
similarity index 100%
rename from figures/Schmidt2017/tex/draw_pops.tex
rename to figures/Schmidt2018/tex/draw_pops.tex
diff --git a/figures/Schmidt2017/tex/indirect_23E.eps b/figures/Schmidt2018/tex/indirect_23E.eps
similarity index 100%
rename from figures/Schmidt2017/tex/indirect_23E.eps
rename to figures/Schmidt2018/tex/indirect_23E.eps
diff --git a/figures/Schmidt2017/tex/indirect_4E23E.eps b/figures/Schmidt2018/tex/indirect_4E23E.eps
similarity index 100%
rename from figures/Schmidt2017/tex/indirect_4E23E.eps
rename to figures/Schmidt2018/tex/indirect_4E23E.eps
diff --git a/figures/Schmidt2017/tex/indirect_4E5E.eps b/figures/Schmidt2018/tex/indirect_4E5E.eps
similarity index 100%
rename from figures/Schmidt2017/tex/indirect_4E5E.eps
rename to figures/Schmidt2018/tex/indirect_4E5E.eps
diff --git a/figures/Schmidt2017/tex/indirect_5E.eps b/figures/Schmidt2018/tex/indirect_5E.eps
similarity index 100%
rename from figures/Schmidt2017/tex/indirect_5E.eps
rename to figures/Schmidt2018/tex/indirect_5E.eps
diff --git a/figures/Schmidt2017/tex/indirect_6E.eps b/figures/Schmidt2018/tex/indirect_6E.eps
similarity index 100%
rename from figures/Schmidt2017/tex/indirect_6E.eps
rename to figures/Schmidt2018/tex/indirect_6E.eps
diff --git a/figures/Schmidt2017/tex/lateral_paths.tex b/figures/Schmidt2018/tex/lateral_paths.tex
similarity index 100%
rename from figures/Schmidt2017/tex/lateral_paths.tex
rename to figures/Schmidt2018/tex/lateral_paths.tex
diff --git a/figures/Schmidt2017/tex/texcolors.tex b/figures/Schmidt2018/tex/texcolors.tex
similarity index 100%
rename from figures/Schmidt2017/tex/texcolors.tex
rename to figures/Schmidt2018/tex/texcolors.tex
diff --git a/multiarea_model/data_multiarea/Model.py b/multiarea_model/data_multiarea/Model.py
index 0d14ab434e504a28baf70bdc6838805e04241a78..19eef02834cc15362feaf680c80cca95452d627d 100644
--- a/multiarea_model/data_multiarea/Model.py
+++ b/multiarea_model/data_multiarea/Model.py
@@ -2,9 +2,9 @@
Model
================
-This script defines the model described in Schmidt et al. (2017).
+This script defines the model described in Schmidt et al. (2018).
The procedures are described in detail in the Methods section of
-Schmidt et al. (2017).
+Schmidt et al. (2018).
It loads the data prepared by VisualCortexData.py and computes
neuronal numbers for each population, the external inputs
to each population and the number of synapses of each connection
@@ -491,7 +491,7 @@ def compute_Model_params(out_label='', mode='default'):
"""
2. Process Binzegger data
The notation follows Eqs. (11-12 and following) in
- Schmidt et al. (2017):
+ Schmidt et al. (2018):
v : layer of cortico-cortical synapse
cb : cell type
cell_layer : layer of the cell
diff --git a/multiarea_model/data_multiarea/VisualCortex_Data.py b/multiarea_model/data_multiarea/VisualCortex_Data.py
index 8aa29389b459dc7a9460fbf016dc9d6a162c999e..9b1deda921e1037599716a76f9c34344ffb64397 100644
--- a/multiarea_model/data_multiarea/VisualCortex_Data.py
+++ b/multiarea_model/data_multiarea/VisualCortex_Data.py
@@ -12,9 +12,9 @@ tasks:
viscortex_processed_data.json.
All details of the procedures in this scripts are described in
-Schmidt M, Bakker R, Hilgetag CC, Diesmann M & van Albada SJ (2017)
+Schmidt M, Bakker R, Hilgetag CC, Diesmann M & van Albada SJ
"Multi-scale account of the network structure of macaque visual cortex"
-Brain Structure and Function (2017)
+Brain Structure and Function (2018), 223:1409
Experimental Data
diff --git a/multiarea_model/multiarea_model.py b/multiarea_model/multiarea_model.py
index d678fe768e66fc129f314264770c4ecfb286c6fc..54cd8da453a9b05327aece2208ef54f4f1a4eb1a 100644
--- a/multiarea_model/multiarea_model.py
+++ b/multiarea_model/multiarea_model.py
@@ -3,7 +3,7 @@ multiarea_model
==============
Network class to instantiate and administer instances of the
-multi-area model of macaque visual cortex by Schmidt el. (2016).
+multi-area model of macaque visual cortex by Schmidt el. (2018).
Classes
-------
@@ -17,7 +17,7 @@ label. As members, it may contain three classes:
- theory : theory class that serves to estimate the stationary state
of the network using mean-field theory
- Schuecker J, Schmidt M, van Albada SJ, Diesmann M, HeliasM(2017)
+ Schuecker J, Schmidt M, van Albada SJ, Diesmann M, Helias M (2017)
Fundamental Activity Constraints Lead to Specific Interpretations of
the Connectome. PLoS Comput Biol 13(2): e1005179.
doi:10.1371/journal.pcbi.1005179
diff --git a/multiarea_model/theory.py b/multiarea_model/theory.py
index f6535054b485fdd464288e6c63f6e633acb5a5f0..23e17b02999dba59a7e2d6d8bdb95d2e9156965d 100644
--- a/multiarea_model/theory.py
+++ b/multiarea_model/theory.py
@@ -3,7 +3,7 @@ theory
============
Theory package to predict the stable fixed points of the multi-area
-model of macaque visual cortex (Schmidt et al. 2015), perform further
+model of macaque visual cortex (Schmidt et al. 2018), perform further
analysis on them and to apply the stabilization procedure (Schuecker,
Schmidt et al., 2017) to the network connectivity.