From 04925ccab640853ad746628b7e3a8d5db980e29c Mon Sep 17 00:00:00 2001
From: Marike Reimer <35542396+MarikeReimer@users.noreply.github.com>
Date: Sat, 6 Jul 2024 08:02:36 -0400
Subject: [PATCH 1/2] Update SONATA_DEVELOPER_GUIDE.md

Doc update adding dendritic spine as Type #5, link to DXplorer, and naming convention proposal.
---
 docs/SONATA_DEVELOPER_GUIDE.md | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/docs/SONATA_DEVELOPER_GUIDE.md b/docs/SONATA_DEVELOPER_GUIDE.md
index 49c4cda..fe060f4 100644
--- a/docs/SONATA_DEVELOPER_GUIDE.md
+++ b/docs/SONATA_DEVELOPER_GUIDE.md
@@ -123,6 +123,7 @@ The format used is SWC ( [http://www.neuronland.org/NLMorphologyConverter/Morpho
   2 - axon
   3 - basal dendrite
   4 - apical dendrite
+  5 - dendritic spine
 
 * IDs must start at 1
 
@@ -150,6 +151,13 @@ The format used is SWC ( [http://www.neuronland.org/NLMorphologyConverter/Morpho
   section plus 1. The order in which sections are assigned an ID is the order
   in which their first segment appears in the file.
 
+* Dendritic spines morphology should follow the guidelines described in the DXplorer framework: https://pubmed.ncbi.nlm.nih.gov/34591770/
+Naming Convention Example: "SpineType"_5.0
+
+An additional segment is needed to describe spines with necks.
+Naming Convention Example: "SpineType"_5.0 and "SpineType"neck_5.0
+
+  
 It is not required that the soma is located at 0,0,0 in the SWC file, but in cases where the morphology has a soma, the soma will be re-centered to 0,0,0 upon loading into the circuit.  Node translations will then be applied to this recentered morphology. This behavior can be overridden by the optional reserved attribute "recenter" for nodes and node_types.  See "Representing networks of neurons" for more details.
 
 It is recommended, but not required, that morphologies in a network have a standardized orientation, so that their orientation vectors in the network can be inferred from node rotation angles.

From cdbbbd9c51669b382cdde3e2be52809badbb4022 Mon Sep 17 00:00:00 2001
From: Marike Reimer <35542396+MarikeReimer@users.noreply.github.com>
Date: Wed, 17 Jul 2024 17:25:22 -0400
Subject: [PATCH 2/2] Update SONATA_DEVELOPER_GUIDE.md

Revise dendritic spine documentation.
---
 docs/SONATA_DEVELOPER_GUIDE.md | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/docs/SONATA_DEVELOPER_GUIDE.md b/docs/SONATA_DEVELOPER_GUIDE.md
index fe060f4..a6eed02 100644
--- a/docs/SONATA_DEVELOPER_GUIDE.md
+++ b/docs/SONATA_DEVELOPER_GUIDE.md
@@ -152,11 +152,14 @@ The format used is SWC ( [http://www.neuronland.org/NLMorphologyConverter/Morpho
   in which their first segment appears in the file.
 
 * Dendritic spines morphology should follow the guidelines described in the DXplorer framework: https://pubmed.ncbi.nlm.nih.gov/34591770/
-Naming Convention Example: "SpineType"_5.0
 
-An additional segment is needed to describe spines with necks.
-Naming Convention Example: "SpineType"_5.0 and "SpineType"neck_5.0
+Naming Convention Example: "5.0_SpineHead"
 
+All dendritic spines have heads,but only some spines have necks.
+
+An additional segment is needed to describe spines with necks. Neck and head numerical prefixes must match.
+
+Naming Convention Example: "5.0_SpineHead" and "5.0_SpineNeck"
   
 It is not required that the soma is located at 0,0,0 in the SWC file, but in cases where the morphology has a soma, the soma will be re-centered to 0,0,0 upon loading into the circuit.  Node translations will then be applied to this recentered morphology. This behavior can be overridden by the optional reserved attribute "recenter" for nodes and node_types.  See "Representing networks of neurons" for more details.