idr0159-strobl-insectlightsheet/idr0159-study.txt at main · IDR/idr0159-strobl-insectlightsheet · GitHub

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# 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]	idr0159
Study Title	Non-invasive long-term fluorescence live imaging of Tribolium
castaneum embryos
Study Type	time-lapse imaging
Study Type Term Source REF	OMIT
Study Type Term Accession	OMIT_0027490
Study Description	Insect development has contributed significantly to our understanding
of metazoan development. However, most information has been
obtained by analyzing a single species, the fruit fly Drosophila
melanogaster. Embryonic development of the red flour beetle
Tribolium castaneum differs fundamentally from that of Drosophila in
aspects such as short-germ development,embryonic leg development,
extensive extra-embryonic membrane formation and non-involuted
head development. Although Tribolium has become the second most
important insect model organism, previous live imaging attempts have
addressed onlyspecific questions and no long-termlive imaging data of
Tribolium embryogenesis have been available. By combining light
sheet-based fluorescence microscopy with a novel mounting method,
we achieved complete, continuous and non-invasive fluorescence live
imaging of Tribolium embryogenesis at high spatiotemporal resolution.
The embryos survived the 2-day or longer imaging process, developed
into adults and produced fertile progeny. Our data document all
morphogenetic processes from the rearrangement of the uniform
blastoderm to the onset of regular muscular movement in the same
embryo and in four orientations, contributing significantly to the
understanding of Tribolium development. Furthermore, we created a
comprehensive chronological table of Tribolium embryogenesis,
integrating most previous work and providing a reference for future
studies. Based on our observations, we provide evidence that serosa
window closure and serosa opening, although deferred by more than
1 day, are linked. All our long-term imaging datasets are available
as a resource for the community. Tribolium is only the second
insect species, after Drosophila, for which non-invasive long-term
fluorescence live imaging has been achieved.
Study Key Words	Arthropod development	Coleoptera	Tribolium castaneum	Serosa scar	Morphogenesis	Embryogenesis	Light sheet-based fluorescence microscopy	LSFM	DSLM
Study Organism	Tribolium castaneum
Study Organism Term Source REF	NCBITaxon
Study Organism Term Accession	7070
Study Experiments Number	1
Study External URL
Study BioImage Archive Accession
Study Public Release Date	2025-02-18

# Study Publication
Study PubMed ID	24803590
Study Publication Title	Non-invasive long-term fluorescence live imaging of Tribolium castaneum embryos
Study Author List	Strobl F, Stelzer EHK
Study PMC ID
Study DOI	https://doi.org/10.1242/dev.108795

# Study Contacts
Study Person Last Name	Strobl
Study Person First Name	Frederic
Study Person Email	frederic.strobl@physikalischebiologie.de
Study Person Address	Goethe University, Buchmann Institute for Molecular Life Sciences, Max-von-Laue-Straße 15, 60438 Frankfurt am Main
Study Person ORCID	0000-0002-5350-0194
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	Strobl et al
Study Data Publisher	University of Dundee
Study Data DOI	https://doi.org/10.17867/10000202

Term Source Name	NCBITaxon	EFO	CMPO	FBbi
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/


# EXPERIMENT SECTION
# Experiment Section containing all information relative to each experiment in the study including materials used, protocols names and description, phenotype names and description. For multiple experiments this section should be repeated.  Copy and paste the whole section below and fill out for the next experiment

Experiment Number	1
Comment[IDR Experiment Name]	idr0159-strobl-insectlightsheet/experimentA
Experiment Sample Type	tissue
Experiment Description	Fluorescence live imaging of a Tribolium castaneum embryo.
Experiment Size	5D Images: 12	Average Image Dimension (XYZCT):	Total Tb:
Experiment Example Images
Experiment Imaging Method	light sheet fluorescence microscopy	SPIM
Experiment Imaging Method Term Source REF	Fbbi
Experiment Imaging Method Term Accession		FBbi_00000369
Experiment Organism
Experiment Organism Term Source REF	NCBITaxon
Experiment Organism Term Accession
Experiment Comments

# assay files
Experiment Assay File	idr0159-experimentA-annotation
Experiment Assay File Format	tab-delimited text
Assay Experimental Conditions
Assay Experimental Conditions Term Source REF
Assay Experimental Conditions Term Accession
Quality Control Description

# Protocols
Protocol Name	growth protocol	treatment protocol	image acquisition and feature extraction protocol	data analysis protocol
Protocol Type	growth protocol	treatment protocol	image acquisition and feature extraction protocol	data analysis protocol
Protocol Type Term Source REF	EFO	EFO
Protocol Type Term Accession	EFO_0003789	EFO_0003969
Protocol Description	We used an advanced variant of LSFM termed monolithic digital scanned laser light sheet-based fluorescence microscopy (mDSLM), which is based on DSLM (Keller and Stelzer, 2010). Parameters are provided in supplementary material Table S1. Imaging started immediately after the embryo was inserted into the sample chamber.	Image processing was performed with Mathematica (Wolfram). Single planes (SP) were used to calculate the maximum projections. With those projections, two processing steps were performed. (1) Background correction (BC). A brightness threshold was applied that distinguishes the specimen from the background. The background was used to calculate the mean image background and then set to zero. Then, the mean image background was subtracted from the whole image. This led to an overall intensity decrease. (2) Mean transform (MT). For the desired series of images, the brightest and the dimmest images were selected and the mean intensity was calculated. For the desired series, the image closest to that intensity was determined and designated the reference image. All images were normalized to match the intensity of the reference image. This included both increase and decrease of intensities (supplementary material Fig. S3). Images that underwent this procedure are marked as maximum projections with image processing (MP). If necessary, images underwent equal brightness adjustment. Further details of image processing can be provided upon request. Images were cropped to 600×1000 pixels (XD×YD, supplementary material Table S1), maintaining the original line and pixel pitches used during the imaging recording process. Cell tracking in Fig. 3B was performed manually. Amira (FEI Visualization Science Group, Düsseldorf, Germany) was used for volume rendering (AV) in Fig. 2D and supplementary material Movie 3. Meta information about the three long-term imaging datasets is provided in supplementary material Table S1 (the original datasets, associated figures and movies in full quality are available at www.physikalischebiologie.de/bugcube).

# Phenotypes
Phenotype Name
Phenotype Description
Phenotype Score Type
Phenotype Term Source REF	CMPO
Phenotype Term Name
Phenotype Term Accession


# Feature Level Data Files (give individual file details unless there is one file per well)
Feature Level Data File Name
Feature Level Data File Format
Feature Level Data File Description
Feature Level Data Column Name
Feature Level Data Column Description

#  Processed Data Files
Processed Data File Name
Processed Data File Format	tab-delimited text
Processed Data File Description
Processed Data Column Name
Processed Data Column Type
Processed Data Column Annotation Level
Processed Data Column Description
Processed Data Column Link To Assay File