idr0051-study.txt

# FILL IN AS MUCH INFORMATION AS YOU CAN.  HINTS HAVE BEEN PUT IN SOME FIELDS AFTER THE HASH # SYMBOL. REPLACE THE HINT WITH TEXT WHERE APPROPRIATE.				
				
# STUDY DESCRIPTION SECTION				
"# Section with generic information about the study including title, description, publication details (if applicable) and contact details"				
				
Comment[IDR Study Accession]	idr0051			
Study Title	In Toto Cell Tracking using Lightsheet Microscopy of the Neuromesodermal Progenitor Zone of the Zebrafish Tailbud from the 21st Somite Stage			
Study Type	time-lapse imaging			
Study Type Term Source REF	OMIT			
Study Type Term Accession	OMIT_0027490			
Study Description	Lightsheet microscopy has been previously used to image and directly study the process of gastrulation in a zebrafish embryo. Before now it was not possible to use this method to study late-stage somatogenesis, due to the movement of the embryo, resulting in displacement from the field of view. Here we achieve 4D lightsheet imaging with online, image based registration to maintain the field of view during long timelapses, with emphasis on the tailbud. The zebrafish tailbud is of special interest as it contains a population of bipotent progenitor cells, neuromesodermal progenitors (NMps), competent to enter either the mesodermal or neural lineages. This dataset provides in toto tracking of the tailbud of the developing zebrafish whilst also demonstrating the potential of online tracking during developing to maintain high magnification images whilst tracking a growing object.		 	
Study Organism	Danio rerio			
Study Organism Term Source REF	NCBITaxon			
Study Organism Term Accession	NCBITaxon_7955			
Study Experiments Number	1			
Study External URL				
Study Public Release Date	2018-11-29			
				
# Study Publication				
Study PubMed ID	30333213			
Study Publication Title	Neuromesodermal progenitors are a conserved source of spinal cord with divergent growth dynamics.			
Study Author List	Attardi A, Fulton T, Florescu M, Shah G, Muresan L, Lenz MO, Lancaster C, Huisken J, van Oudenaarden A, Steventon B			
Study PMC ID	PMC6240315			
Study DOI	https://doi.org/10.1242/dev.166728			
				
# Study Contacts				
Study Person Last Name	Steventon			
Study Person First Name	Benjamin			
Study Person Email	bjs57@cam.ac.uk			
Study Person Address	Department of Genetics University of Cambridge			
Study Person ORCID	https://orcid.org/0000-0001-7838-839X			
Study Person Roles	submitter			
				
# Study License and Data DOI				
Study License	CC BY 4.0			
Study License URL	https://creativecommons.org/licenses/by/4.0/			
Study Copyright	Steventon et al.			
Study Data Publisher	University of Dundee			
Study Data DOI	https://doi.org/10.17867/10000117			
				
Term Source Name	NCBITaxon	EFO	CMPO	FBbi	OMIT
Term Source URI	http://purl.obolibrary.org/obo/	http://www.ebi.ac.uk/efo/	http://www.ebi.ac.uk/cmpo/	http://purl.obolibrary.org/obo/	http://purl.obolibrary.org/obo/
				
				
# EXPERIMENT SECTION							
				
Experiment Number	1			
Comment[IDR Experiment Name]	idr0051-fulton-tailbudlightsheet/experimentA	
Experiment Sample Type	tissue
Experiment Description	Lightsheet imaging of tailbud from 18 somite stage with one frame per 2 minutes			
Experiment Size	5D Images: 	XYZ 1x1x1 1channel 120seconds/frame	Total Tb: 	0.5
Experiment Example Images	180712_H2B_22ss_Courtney1_20180712-163837_p00_c00_t0000.ome.tiff			
Experiment Imaging Method	light sheet fluorescence microscopy	SPIM			
Experiment Imaging Method Term Source REF	Fbbi			
Experiment Imaging Method Term Accession	FBbi_00000369			
Experiment Comments	Detailed annotation of the mounting and imaging technique used in production of this dataset is available from Development (doi: 10.1242/dev.166728) and Wellcome Trust Open Research (DOIXXXXXXXXXXXX)			
				
# assay files				
Experiment Assay File	# put in the name of the assay file			
Experiment Assay File Format	tab-delimited text			
Assay Experimental Conditions	28 Degrees ambiant CO2 E3 Media 			
Assay Experimental Conditions Term Source REF	# leave blank			
Assay Experimental Conditions Term Accession	# leave blank			
Quality Control Description	Manual validation of a selection of tracks undertaken described in Development doi: 10.1242/dev.166728			
				
# Protocols				
Protocol Name	growth protocol	treatment protocol	image aquistion and feature extraction protocol	data analysis protocol
Protocol Type	growth protocol	treatment protocol	image aquistion and feature extraction protocol	data analysis protocol
Protocol Type Term Source REF	EFO	EFO		
Protocol Type Term Accession	EFO_0003789	EFO_0003969		
Protocol Description	# text about how the cells were grown here	# text about any specific treatment to the cells here	Detailed annotation of the mounting and imaging technique used in production of this dataset is avalible from Development (doi: 10.1242/dev.166728) and Wellcome Trust Open Research (DOIXXXXXXXXXXXX)	TGMM Tracking on nuclei with manual validaition using FIJI plugin Mamut
				
# Phenotypes				
Phenotype Name	# if any specific phenotypes were identified in the experiment enter the information here.  Each phenotype should be in a separate column.			
Phenotype Description	"# give a brief description of each phenotype, or how it was determined e.g. if score X is greater than Y then this phenotype assigned."			
Phenotype Score Type	"# choose from: manual, automatic"			
Phenotype Term Source REF	CMPO			
Phenotype Term Name	# if your phenotype matches a term in the Cellular Microscopy Phenotype Ontology enter it here http://www.ebi.ac.uk/CMPO			
Phenotype Term Accession	# if your phenotype matches a term in the Cellular Microscopy Phenotype Ontology enter the accession for the term here http://www.ebi.ac.uk/CMPO		 	
				
				
# Feature Level Data Files (give individual file details unless there is one file per well)				
Feature Level Data File Name	# list any feature level table files here			
Feature Level Data File Format	# a description of the table			
Feature Level Data File Description	# tab-delimited text or other format			
Feature Level Data Column Name	"# list all the columns in the table, each column in the table should be in a separate column here"			
Feature Level Data Column Description	# describe the values in each column			
				
#  Processed Data Files 				
Processed Data File Name	GMEMfinalResult_frame*.xml			
Processed Data File Format	tab-delimited text			
Processed Data File Description	Tracking data as .xml filetypes containging coodinates of each cell at each timepoint with one .xml per timepoint			
Processed Data Column Name	"# list each of the columns in the processed data file here, each column in the table should be ain a separate column here"			
Processed Data Column Type	"# state the type of value in each column. Choose from: location, reagent identifier, gene identifier, gene symbol, gene description, data, phenotype, experimental condition"			
Processed Data Column Annotation Level	"# for data and phenotype columns enter the level of the annotation so that it is clear if the value is derived from data from a image, is averaged over many images. E.g. gene, experimental condition"			
"experimental condition and gene, phenotype, image, protein"""				
Processed Data Column Description	"# for each data and phenotype column, enter a brief description of what the value represents"			
Processed Data Column Link To Assay File	"# enter which column can be used to link the information in the processed data file to the assay file e.g. targeted protein, or gene identifier"