STOMATA LEVEL README text document

OBJECTIVES
Gather and analyze phenotype data relating to WUE in sagebrush seedlings, specifically, stomata density and size on both leaf surfaces.

PERSONNEL
Carlos Dave Dumaguit, Boise State University, Boise, ID, USA
carlosdavedumagu@boisestate.edu

Principal Investigator: Sven Buerki, Ph.D., Boise State University, Boise, ID, USA
svenbuerki@boisestate.edu

Stephanie Rood, undergraduate student intern

Walker Morales, undergraduate student intern

FUNDING
US National Science Foundation and Idaho EPSCoR: OIA-1757324

DATA COLLECTION
Data was collected by imaging Artemisia tridentata seedling leaves following the Stomata Phenotyping protocol developed for this project.
All raw images were taken in the Summer of 2021.
Images of leaves were taken on a Leica model CME microscope with images captured by a Motic Moticam X3 microscope camera. 
Three images at 10x objective lens were captured on each surface of every leaf. 
Two more images were taken at 40x objective lens within the confines of each 10x image. 
These two images focused on capturing higher resolution examples of stomata for dimension measurements.
Light microscope images of leaves were first processed in R to standardize size and add grid markings to each image for scoring. 
Count data was gathered within a 1000 um X 600 um area, recording data in Microsoft Excel for each sample. 
Measurements of stomata dimensions were gathered using the vector line tool within image software FIJI/ImageJ using the 40x images.

STANDARDS
SI - Systeme International (Metric system)

SOFTWARE(S)
R Core Team (2022). R: A language and environment for statistical computing. R Foundation for Statistical
Computing, Vienna, Austria. URL https://www.R-project.org/.
Rasband, W.S., ImageJ, U. S. National Institutes of Health, Bethesda, Maryland, USA, https://imagej.nih.gov/ij/, 1997-2018. 

DATA STRUCTURE
Root folder: 'https://www.northwestknowledge.net/data/92558821-2d5a-4e43-8a96-086c77e564c9/'
	'./Stomata/00_Raw_data/' - This folder contains the raw image data for this project and associated scripts.
	'./Stomata/00_Raw_data/data/' - This folder contains the image and datasheets of stomata which is structured into folders corresponding to unqiue sample IDs.
	'./Stomata/00_Raw_data/Functions/' - Folder of R scripts with user defined functions.
	'./Stomata/00_Raw_data/Stomata_script.R' - R script to generate and update databases for stomata data.

PROCESSING PROCEDURES/PROTOCOLS
Stomata phenotyping protocol ###need copy of this protocol

KNOWN PROBLEMS/LIMITATIONS

CITATION INSTRUCTIONS
Dumaguit CDC, Buerki S. 2023. Sagebrush greenhouse water use efficiency GxE phenotypic data [dataset]. University of Idaho. https://doi.org/10.7923/jk5q-6876

IP & LICENSING
Creative Commons Attribution 4.0 International ([CC-BY 4.0])(https://creativecommons.org/licenses/by/4.0/legalcode)