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idr0079-study.txt
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idr0079-study.txt
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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] idr0079
Study Title An Image-Based Data-Driven Analysis of Cellular Architecture in a Developing Tissue
Study Type microscopy assay
Study Type Term Source REF EFO
Study Type Term Accession EFO_0002909
Study Description A data-driven analysis of cell morphology and intracellular organization in the developing zebrafish posterior lateral line primordium, a model tissue for the study of self-organized morphogenesis. 3D image stacks were acquired using AiryScan FAST-mode confocal fluorescence microscopy. Automated single-cell segmentation and point cloud-based morphometry were developed to extract numerical features representing cell morphology and intracellular protein distributions. Machine learning was used with the extracted numerical features to perform data integration across experiments and context-guided data visualization. The resulting data was analyzed to discover biologically meaningful patterns at the cell and tissue scale.
Study Key Words image analysis cellular morphometry morphogenesis lateral line primordium data integration context-guided visualization
Study Organism Danio rerio
Study Organism Term Source REF NCBITaxon
Study Organism Term Accession 7955
Study Experiments Number 2
Study External URL github.com/WhoIsJack/data-driven-analysis-lateralline
Study BioImage Archive Accession
Study Public Release Date 2020-06-30
# Study Publication
Study PubMed ID 32501214
Study Publication Title An Image-Based Data-Driven Analysis of Cellular Architecture in a Developing Tissue
Study Author List Hartmann J, Wong M, Gallo E, Gilmour D
Study PMC ID PMC7274788
Study DOI https://doi.org/10.7554/eLife.55913
# Study Contacts
Study Person Last Name Hartmann Gilmour
Study Person First Name Jonas Darren
Study Person Email [email protected] [email protected]
Study Person Address Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany Institute of Molecular Life Sciences, University of Zurich (UZH), Zurich, Switzerland
Study Person ORCID 0000-0002-5600-8285
Study Person Roles submitter, study lead principal investigator
# Study License and Data DOI
Study License CC BY 4.0
Study License URL https://creativecommons.org/licenses/by/4.0/
Study Copyright Hartmann et al
Study Data Publisher University of Dundee
Study Data DOI https://doi.org/10.17867/10000138
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] idr0079-hartmann-lateralline/experimentA
Experiment Data DOI https://doi.org/10.17867/10000138a
Experiment Sample Type tissue
Experiment Description 3D confocal live imaging of the zebrafish posterior lateral line primordium labeled with the membrane marker cldnB:lyn-EGFP for segmentation and optionally with one of several additional labels.
Experiment Size 5D Images: 165 Average Image Dimension (XYZCT): 1625 x 810 x 141 x 2 x 1 Total Tb: 0.113
Experiment Example Images D2470961E8
Experiment Imaging Method array-scan confocal microscopy
Experiment Imaging Method Term Source REF Fbbi
Experiment Imaging Method Term Accession Fbbi_00000393
Experiment Comments AiryScan FAST-mode confocal fluorescence microscopy
# assay files
Experiment Assay File idr0079-experimentA-assays.txt
Experiment Assay File Format tab-delimited text
Assay Experimental Conditions
Assay Experimental Conditions Term Source REF
Assay Experimental Conditions Term Accession
Quality Control Description Single-cell segmentation quality was checked manually for samples where a large number of cells (>20%) failed to be recognized by the algorithm.
# Protocols
Protocol Name growth protocol image acquisition and feature extraction protocol data analysis protocol
Protocol Type growth protocol image acquisition and feature extraction protocol data analysis protocol
Protocol Type Term Source REF EFO
Protocol Type Term Accession EFO_0003789
Protocol Description Zebrafish embryos were grown in E3 buffer at 27-30C according to standard procedures (see zfin.org/zf_info/zfbook/zfbk.html). Where applicable, mRNA for reporter gene expression was injected at the 1-cell stage. Pigmentation was prevented by treating embryos with 0.002% N-phenylthiourea (PTU) starting at 25hpf. Embryos expressed the transgenic membrane label cldnb:lyn-EGFPR (see doi.org/10.1016/j.devcel.2006.02.019) and in most cases one of several additional red fluorescence markers (see Experiment Assay File). Where applicable, lysosomes were stained by treating embryos with 1?M LysoTracker Deep Red in E3 medium with 1% DMSO for 90 minutes prior to mounting. For imaging, embryos were dechorionated manually, anaesthetized with 0.01% Tricaine and mounted in 1% peqGOLD Low Melt Agarose in E3 containing 0.01% Tricaine in a MatTek Glass Bottom Microwell Dish (35mm Petri dish, 10mm microwell, 0.16-0.19mm coverglass). Imaging was performed on the Zeiss LSM880 AiryScan confocal microscope in FAST mode with a 40X 1.2NA water objective with Immersol W immersion fluid. Deconvolution was performed using the ZEN Black Software's 3D AiryScan deconvolution with 'auto' settings. Where appropriate, linear unmixing of channel bleed-through was performed as described in the Study Publication. Automated single-cell segmentation was performed using a custom python pipeline based on thresholding and watershed expansion, described in detail in the Study Publication. Numerical features describing cell morphology and subcellular protein distributions were computed for each segmented cell using a point cloud-based morphometry approach. Protein distribution features were then cross-predicted between datasets using machine learning based on cell shape features as input. RNA spot counts from pea3 single molecule Fluorescence In-Situ Hybridization (see experiment B) were similarly predicted for each cell in all other samples. To provide biological context for analysis and visualization, specific biologically relevant cellular archetypes were manually annotated in some samples and then again cross-predicted for all cells based on cell shape features. Custom pipelines and algorithms for these analyses were implemented in python and are described in detail in the Study Publication.
# Phenotypes
Phenotype Name
Phenotype Description
Phenotype Score Type
Phenotype Term Source REF
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 idr0079-experimentA-processed.txt
Processed Data File Format tab-delimited text
Processed Data File Description A list of all data files in the extracted_measurements folder, describing the data contained in each of these files
Processed Data Column Name Source Name File Name File Path Description File Structure Notes
Processed Data Column Type
Processed Data Column Annotation Level
Processed Data Column Description
Processed Data Column Link To Assay File Source Name
Experiment Number 2
Comment[IDR Experiment Name] idr0079-hartmann-lateralline/experimentB
Experiment Data DOI https://doi.org/10.17867/10000138b
Experiment Sample Type tissue
Experiment Description 3D confocal imaging of fixed samples of the zebrafish posterior lateral line primordium labeled with the membrane marker cldnB:lyn-EGFP and stained for pea3 mRNA using single molecule Fluorescence In-Situ Hybridization (smFISH).
Experiment Size 5D Images: 31 Average Image Dimension (XYZCT): 1572 x 780 x 117 x 2 x 1 Total Tb: 0.0166
Experiment Example Images 80759AC74C
Experiment Imaging Method array-scan confocal microscopy
Experiment Imaging Method Term Source REF Fbbi
Experiment Imaging Method Term Accession Fbbi_00000393
Experiment Comments AiryScan FAST-mode confocal fluorescence microscopy
# assay files
Experiment Assay File idr0079-experimentB-assays.txt
Experiment Assay File Format tab-delimited text
Assay Experimental Conditions
Assay Experimental Conditions Term Source REF
Assay Experimental Conditions Term Accession
Quality Control Description Single-cell segmentation quality was checked manually for samples where a large number of cells (>20%) failed to be recognized by the algorithm.
# Protocols
Protocol Name growth protocol image acquisition and feature extraction protocol data analysis protocol
Protocol Type growth protocol image acquisition and feature extraction protocol data analysis protocol
Protocol Type Term Source REF EFO
Protocol Type Term Accession EFO_0003789
Protocol Description Zebrafish embryos were grown in E3 buffer at 27-30C according to standard procedures (see zfin.org/zf_info/zfbook/zfbk.html). Pigmentation was prevented by treating embryos with 0.002% N-phenylthiourea (PTU) starting at 25hpf. Embryos expressed the transgenic membrane label cldnb:lyn-EGFPR (see doi.org/10.1016/j.devcel.2006.02.019) and were stained for pea3 mRNA with smFISH. For smFISH staining, embryos were fixed in 4% PFA in PBS-T, permeabilized in 100% methanol overnight, rehydrated with a methanol series and finally hybridized with pea3 probe solution overnight. See the Study Publication for further details, including washing steps, buffer compositions and probe sequences. For imaging, embryos were mounted on glass slides using VECTASHIELD HardSet Antifade Mounting Medium. Imaging was performed on the Zeiss LSM880 AiryScan confocal microscope in FAST mode with a 63x 1.4NA oil immersion objective. 8x averaging was used specifically for the smFISH channel. Deconvolution was performed using the ZEN Black Software's 3D AiryScan deconvolution with 'auto' settings. Automated single-cell segmentation was performed using a custom python pipeline based on thresholding and watershed expansion, described in detail in the Study Publication. Numerical features describing cell morphology were computed for each segmented cell using a point cloud-based morphometry approach. smFISH spots were identified using the `blob_log` spot detector from the scikit-image library for python. Protein distribution features were cross-predicted from other datasets (see experiment A) using machine learning based on cell shape features as input. Custom pipelines and algorithms for these analyses were implemented in python and are described in detail in the Study Publication.
# Phenotypes
Phenotype Name
Phenotype Description
Phenotype Score Type
Phenotype Term Source REF
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 idr0079-experimentB-processed.txt
Processed Data File Format tab-delimited text
Processed Data File Description A list of all data files in the extracted_measurements folder, describing the data contained in each of these files
Processed Data Column Name Source Name File Name File Path Description File Structure Notes
Processed Data Column Type Processed Data Column Annotation Level
Processed Data Column Description
Processed Data Column Link To Assay File Source Name