assays/Weather_Data/README.md

+#### Weather Data
+
+Weather data over the course of the field experiment from 26 September 2019 to 28 February 2020 collected by a meteorological station at the INIA-Huasco experimental center in the southern Atacama Desert (Vallenar, Chile, 28°34′ S, 70°47′ W and 469 m.a.s.l.) 300 m from the field trial and by soil sensors in the field trial;
+
+
+<img src= "Dumschott_et_al_Weather_Data.png" alt="Weather Data" width= "500">
+
+
+ (a) daily maximum and night mean temperature; <br> (b) daily maximum vapor pressure deficit (VPD);<br> (c) daily total radiation;<br> (d) daily mean volumetric soil water content (VSWC). <br>
+ 
+ >**The full irrigation and reduced irrigation treatments started at branching (35 days after sowing), but the sensor data were only available from 40 days after sowing. The colors in the figure represent the respective quinoa developmental stages.**
\ No newline at end of file

assays/Weather_Data/protocols/Weather_data_collection.md

+# Weather Data Collection
+
+- Weather data was collected via meteorlogical station located at the INIA-Huasco experimental setup, approximately 200 meters from the field trial.
+- Measurements of temperature (°C), vapor-pressure deficit (kPa), radiation (W/m2), precipitation, relative humidity were recorded every hour
+
+## Soil Data
+
+- Two soil sensors (one located in the FI plots and one located in the RI plots) recorded volumetric water content and temperature.

studies/ExperimentalSetup/README.md

+# Experimental Setup
+
+**Field Trial Location:** 
+- The trial took place at the INIA-Huasco experimental center located in the southern Atacama Desert (Vallenar, Chile, 28°34′ S, 70°47′ W and 469 m.a.s.l.) during the 2019/2020 growing season (sowing on 26 September 2019, harvest on 21 February 2020).
+- The Atacama desert is one of the driest regions in the world, ensuring that rainfall would not influence the irritation treatment of the experiment.
+
+**Soil Characteristics:** 
+- Sandy loam textural class, composed of sand (75.5%), silt (10.9%) and clay (13.7%), with a low organic matter content (2.0%), an alkaline pH (8.1), slight salinity (2.4 dS m−1), and with a basic content of N-P-K (45-21-311 mg kg−1 respectively)
+
+**Experimental Design:**
+- Nine coastal lowland self-pollinated quinoa lines (CLS-1 to CLS-9) and one commercial cultivar (cv Regalona)
+- Plots here 2 x 4 m and contained four rows of quinoa with an inter-row spacing of 0.5 m
+- Three plots of each line were sown for each treatment.
+- Seeds were sown at a density of 15 kg ha−1 with >85% germination.
+- Two treatments: 
+    - <ins>Full Irrigation (FI):</ins> Considered the reposition of ET<sub>0</sub> and the lack of a crop coefficient (K<sub>c</sub>) for quinoa growing in the region.
+    - <ins>Reduced Irrigation (RI):</ins> Defined a severe reduction of irrigation time (50%) and kept the same schedule as for the full irrigation treatment (every second or third day) by means of pressurized drip lines. RI treatment started at growth stage 20 (branching, extended BBCH).
+- Fertilizer was provided at sowing (75-120-60 N-P-K) and an additional 75 N was provided at growth stage 12 (second pair of leaves visible, extended BBCH).
+- Chlorothalonil (2 L ha−1 BRAVO 720, Syngenta) was applied from growth stage 16 (six pairs of leaves visible, extended BBCH) to manage disease.
+
+
+## Figure: Field trial plot layout
+
+<p float="left">
+  <img src="trialplots_quinoa.png" width="70%" />
+  
+</p>
+
+## Data Collected & Corresponding Assays
+
+#### Data recorded throughout the trial:
+
+- **Weather data:** Collected via meteorlogical station located at the INIA-Huasco experimental setup, approximately 200 meters from the trial.
+    -  See Assay: [Weather_Data](https://git.nfdi4plants.org/usadellab/quinoa_chileanfieldtrial/-/tree/main/assays/Weather_Data?ref_type=heads)    
+
+- **Soil sensors:** Recorded volumetric water content and temperature (located at the yellow stars in the figure above).
+     -  See Assay: [Weather_Data](https://git.nfdi4plants.org/usadellab/quinoa_chileanfieldtrial/-/tree/main/assays/Weather_Data?ref_type=heads)
+
+- **Phenological traits:** Determined visually via regular inspections of the trial using the extended BBCH scale by Sosa-Zúñiga et al. 2017 [1].
+    - See Assay: [Phenology](https://git.nfdi4plants.org/usadellab/quinoa_chileanfieldtrial/-/tree/main/assays/Phenology?ref_type=heads) 
+
+#### Data Collected at the visible inflorescence stage of development (BBCH 59); 46-50 days after sowing:
+
+- **Morphological traits:** Collected for all plots of both treatments on day 47 and included measurements such as plant height and stem diameter.
+     -  See Assay: [Morphology](https://git.nfdi4plants.org/usadellab/quinoa_chileanfieldtrial/-/tree/main/assays/Morphology)
+
+ - **Leaf relative water content:** Collected for all plots of both treatments on day 47.
+    -  See Assay: [Relative_Water_Content](https://git.nfdi4plants.org/usadellab/quinoa_chileanfieldtrial/-/tree/main/assays/RelativeWaterContent?ref_type=heads)    
+
+- **Thermal infrared imaging:** Collected images according to table below.
+    -   See Assay: [Imaging](https://git.nfdi4plants.org/usadellab/quinoa_chileanfieldtrial/-/tree/main/assays/Imaging?ref_type=heads)
+
+| **Sampling Days** | **Blocks** |
+| :------: | ------ |
+| Day 46 (afternoon)| All plots |
+| Day 47 (afternoon)| All plots |
+| Day 47 (late morning*)| All plots |
+|Day 48 (afternoon)|2 and 5|
+|Day 49 (afternoon)|1 and 4|
+|Day 50 (afternoon)|3 and 6|
+
+*leaves were still wet with morning dew. 
+
+Blocks represented differences in the date and time of imaging, they were referred to as repetitions with blocks 1 and 4 assigned to repetition 1, blocks 2 and 5 to repetition 2, and blocks 3 and 6 to repetition 3. Plots were always captured in treatment pairs (RI after FI or vice versa).
+
+- **Hyperspectral imaging:** Collected images according to table below.
+
+    - See Assay: [Imaging](https://git.nfdi4plants.org/usadellab/quinoa_chileanfieldtrial/-/tree/main/assays/Imaging?ref_type=heads)
+
+| **Sampling Days** | **Blocks** |
+| :------: | ------ |
+| Day 46 (afternoon)| All plots |
+| Day 47 (afternoon)| All plots |
+| Day 47 (late morning)| All plots |
+|Day 48 (between 15:00 and 16:00)|2 and 5|
+|Day 49 (between 15:00 and 16:00)|1 and 4|
+|Day 49 (between 16:00 and 17:00)|3 and 6|
+
+Blocks represented differences in the date and time of imaging, they were referred to as repetitions with blocks 1 and 4 assigned to repetition 1, blocks 2 and 5 to repetition 2, and blocks 3 and 6 to repetition 3. Plots were always captured in treatment pairs (RI after FI or vice versa).
+
+- **Chlorophyll fluorescence:** Collected according to table below.
+
+    - See Assay: [Chlorophyll_Fluorescence](https://git.nfdi4plants.org/usadellab/quinoa_chileanfieldtrial/-/tree/main/assays/Chlorophyll_Fluorescence?ref_type=heads)
+    
+
+| Sampling Days | Blocks |
+| ------ | ------ |
+| Dat 48 (between 15:00 and 17:00) | 2 and 5 | 
+|Day 49 (between 14:45 and 15:45 ) | 1 and 4 |
+| Day 50 (between 10:24 and 12:49) | All plots|
+
+#### Data Collected at Harvest:
+
+- Seed and panicle metrics were collected when plants reached physiological maturity
+    
+    - See Assay: [Harvest](https://git.nfdi4plants.org/usadellab/quinoa_chileanfieldtrial/-/tree/main/assays/Harvest)
+
+## References
+
+[1] Sosa-Zuniga, V.; Brito, V.; Fuentes, F.; Steinfort, U. Phenological growth stages of quinoa (Chenopodium quinoa) based on the BBCH scale. Ann. Appl. Biol. 2017, 171, 117–124. 
\ No newline at end of file

studies/README.md

-# Experimental Setup
+This ARC consists of one study- a field trial conducted at the INIA-Huasco experimental center located in the southern Atacama Desert (Vallenar, Chile, 28°34′ S, 70°47′ W and 469 m.a.s.l.) during the 2019/2020 growing season (sowing on 26 September 2019, harvest on 21 February 2020).
 
-**Field Trial Setting:** 
-- The trial took place at the INIA-Huasco experimental center located in the southern Atacama Desert (Vallenar, Chile, 28°34′ S, 70°47′ W and 469 m.a.s.l.) during the 2019/2020 growing season (sowing on 26 September 2019, harvest on 21 February 2020).
-- The Atacama desert is one of the driest regions in the world, ensuring that rainfall would not influence the irritation treatment of the experiment.
+Please view the [Experimental Setup](https://git.nfdi4plants.org/usadellab/quinoa_chileanfieldtrial/-/tree/main/studies/ExperimentalSetup?ref_type=heads) for a full description.
 
-**Soil Characteristics:** 
-- Sandy loam textural class, composed of sand (75.5%), silt (10.9%) and clay (13.7%), with a low organic matter content (2.0%), an alkaline pH (8.1), slight salinity (2.4 dS m−1), and with a basic content of N-P-K (45-21-311 mg kg−1 respectively)
 
-**Experimental Design:**
-- Nine coastal lowland self-pollinated quinoa lines (CLS-1 to CLS-9) and one commercial cultivar (cv Regalona)
-- Plots here 2 x 4 m and contained four rows of quinoa with an inter-row spacing of 0.5 m
-- Three plots of each line were sown for each treatment.
-- Seeds were sown at a density of 15 kg ha−1 with >85% germination.
-- Two treatments: 
-    - <ins>Full Irrigation (FI):</ins> Considered the reposition of ET<sub>0</sub> and the lack of a crop coefficient (K<sub>c</sub>) for quinoa growing in the region.
-    - <ins>Reduced Irrigation (RI):</ins> Defined a severe reduction of irrigation time (50%) and kept the same schedule as for the full irrigation treatment (every second or third day) by means of pressurized drip lines. RI treatment started at growth stage 20 (branching, extended BBCH).
-- Fertilizer was provided at sowing (75-120-60 N-P-K) and an additional 75 N was provided at growth stage 12 (second pair of leaves visible, extended BBCH).
-- Chlorothalonil (2 L ha−1 BRAVO 720, Syngenta) was applied from growth stage 16 (six pairs of leaves visible, extended BBCH) to manage disease.
-- Weather data was collected via meteorlogical station located at the INIA-Huasco experimental setup, approximately 200 meters from the trial.
-- Soil sensors (located at the yellow stars in the figure below) recorded volumetric water content and temperature.
+<p float="left">
+  <img src="Quinoaimage8.jpeg" width="40%" />
+  <img src="Quinoaimage3.jpeg" width="50%" /> 
   
-## Figure: Field trial plot layout
-
-![Quinoaplots](quinoa_trialplots.png)
+</p>