From bf2ae6ebc338a97c2553e6e77c0d202e7fe66704 Mon Sep 17 00:00:00 2001
From: Kathryn Dumschott <k.dumschott@fz-juelich.de>
Date: Wed, 11 Jun 2025 12:53:56 +0000
Subject: [PATCH] Edit README.md

---
 assays/MiniPam/README.md | 18 ++++++++++++++++--
 1 file changed, 16 insertions(+), 2 deletions(-)

diff --git a/assays/MiniPam/README.md b/assays/MiniPam/README.md
index 46c486c..ec7b7be 100644
--- a/assays/MiniPam/README.md
+++ b/assays/MiniPam/README.md
@@ -1,4 +1,6 @@
-#### Chlorophyll fluorescence
+# Chlorophyll fluorescence
+
+## Assay Description and Instrumentation
 
 Fluorescence data was collected using a MINI-PAM-II fluorometer (Walz Heinz GmbH, Effeltrich,
 Germany). 
@@ -8,7 +10,7 @@ Germany).
   <img src="Quinoaimage4.jpeg" width="40%" />
 </p>
 
-**To conduct measurements:**
+### Protocol
 
 - The leaf clip was attached to a leaf and measurements of
 photosynthetically active radiation (PAR) and the photosynthetic efficiency of photosystem II (PhiPSII) were
@@ -22,8 +24,11 @@ recorded.
 measured 48 days after sowing between 15:00 and 17:00. All blocks were measured 50 days after sowing
 between 10:24 and 12:49.**
 
+### Calibration and Quality Control
 The fluorescence kinetics of saturation pulse analyses for measurements were inspected using WinControl-3 Software (version 3.29-rev.1112) (Walz Heinz GmbH, Effeltrich, Germany).
 Measurements that did not pass inspection were discarded from subsequent analyses.
+
+### Data Processing
 PhiPSII values were clustered according to genotype, treatment and PAR level using custom R scripts.
 
 **PAR was divided into four levels:**
@@ -34,6 +39,15 @@ PhiPSII values were clustered according to genotype, treatment and PAR level usi
 
 Agglomerative hierarchical clustering was applied on the scaled PhiPSII means for all plots using the ‘agnes’ function of the R package ‘cluster’ [1] with a cut-off of five clusters.
 
+### Software and tools
+
+-  WinControl-3 Software (version 3.29-rev.1112) (Walz Heinz GmbH, Effeltrich, Germany)
+- R (with package 'cluster')
+
+### Assay Date
+
+This assay was performed at the visible inflorescence stage of development (BBCH 59); 46-50 days after sowing
+
 Reference:
 
 [1] Maechler, M.; Rousseeuw, P.; Struyf, A.; Hubert, M.; Hornik, K.; Studer, M.; Roudier, P.; Gonzalez, J.; Kozlowski, K.; Schubert, E.; et al. “Finding Groups in Data”: Cluster Analysis Extended Rousseeuw et al. Available online: https://cran.r-project.org/web/packages/cluster/cluster.pdf (accessed on 26 February 2021).
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