TOWARDS(OPEN(DATAIN(CELL( MIGRATION(RESEARCH( · 2017-06-07 · CCBYSA4.0...
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Transcript of TOWARDS(OPEN(DATAIN(CELL( MIGRATION(RESEARCH( · 2017-06-07 · CCBYSA4.0...
TOWARDS OPEN DATA IN CELL MIGRATION RESEARCH
@pcmasuzzo
paola.masuzzo@vib-‐ugent.be
CC BY-‐SA 4.0
60
STATISTICS SAY I HAVE
SECONDS to capture your
attention
h5ps://de.wikipedia.org/wiki/Datei:Hourglass_2.svg, CC BY-‐SA 3.0
h5ps://t.co/UKmqZQvbHK -‐ tweet by @myusuf3
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Diversity and complexity of cell migration data CMSO: community standards for cell migration research biotracks: a standard format for cell tracking data
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Diversity and complexity of cell migration data CMSO: community standards for cell migration research biotracks: a standard format for cell tracking data
CC BY-‐SA 4.0
Cell migraPon is involved in many processes
Masuzzo, PhD thesis, 2016
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Cell migraPon is involved in many processes
Masuzzo, PhD thesis, 2016
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Cells are able to move following many and diverse strategies
Collec6ve migra6on
Mul6cellular streaming
Mesenchymal
Amoeboid (blebs)
Amoeboid (pseudopodia, filopodia)
INDIVIDUAL MIGRATION
COLLECTIVE MIGRATION
Adapted from Friedl, J. Exp. Med., 2010
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Many study models are used to elucidate the complex mechanisms behind cell movement
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Many study models are used to elucidate the complex mechanisms behind cell movement
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sample preparaPon
image acquisiPon
image processing
data analysis
Servier Medical Art, CC-‐BY 3.0; Cell Image Library, CC-‐BY 3.0
An imaging-‐based cell migraPon experimental workflow has diverse steps
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Servier Medical Art, CC-‐BY 3.0; Cell Image Library, CC-‐BY 3.0; h5ps://commons.wikimedia.org/
These steps produce rich data sets represented in various file formats
sample preparaPon
image acquisiPon
image processing
data analysis
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Breaking down technical barriers means facilitaPng data sharing
Image credit: Ainsley Seago, PLoS Biology
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Data sharing in turn means more analyPcal possibiliPes
h5ps://mulPmot.org/ Masuzzo, Trends in Cell Biology, 2015
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The first step towards data sharing is standardizaPon
Masuzzo, Trends in Cell Biology, 2016
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Diversity and complexity of cell migration data CMSO: community standards for cell migration research biotracks: a standard format for cell tracking data
CC BY-‐SA 4.0
Different informaPon units require specific standardizaPon tasks
raw data & metadata
set up experiment: annotate
invesPgaPon, study, assay
convert processed and derived data into standard
formats
process raw data
convert raw data & metadata into
standard formats
analyze data
experiment
CC BY-‐SA 4.0
Different informaPon units require specific standardizaPon tasks
raw data & metadata
set up experiment: annotate
invesPgaPon, study, assay
convert processed and derived data into standard
formats
process raw data
convert raw data & metadata into
standard formats
analyze data
experiment
data re-‐analysis
data re-‐use
data re-‐purpose
CC BY-‐SA 4.0
CMSO is a young community developing standards for cell migraPon research
h5ps://cmso.science/ h5ps://github.com/CellMigStandOrg
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CMSO is a young community developing standards for cell migraPon research
h5ps://cmso.science/ h5ps://github.com/CellMigStandOrg
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CMSO is re-‐using and adapPng some of the standards available in the community
ISA OME ?
h5p://isa-‐tools.org/ h5p://www.openmicroscopy.org/site
experimental setup
imaging data and metadata
analyPcal results
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And it is developing new standards for cell migraPon-‐specific informaPon
ISA OME biotracks
h5ps://cellmigstandorg.github.io/Tracks/ h5ps://github.com/CellMigStandOrg/biotracks
experimental setup
imaging data and metadata
analy6cal results
CC BY-‐SA 4.0
Diversity and complexity of cell migration data CMSO: community standards for cell migration research biotracks: a standard format for cell tracking data
CC BY-‐SA 4.0
biotracks: tabular data packages for cell tracking files
h5ps://pypi.python.org/pypi/biotracks h5ps://github.com/CellMigStandOrg/biotracks
objects
links
tracks
segmentaPon algorithm
linking algorithm
connecPng links
frame 1 frame 2 frame 3 frame 4 frame 5
* * spliQng event
CC BY-‐SA 4.0
biotracks: tabular data packages for cell tracking files
objects
links
tracks
segmentaPon algorithm
linking algorithm
connecPng links
frame 1 frame 2 frame 3 frame 4 frame 5
* * spliQng event
CC BY-‐SA 4.0
biotracks: tabular data packages for cell tracking files
h5p://fricPonlessdata.io/data-‐packages/
objects
links
tracks
segmentaPon algorithm
linking algorithm
connecPng links
frame 1 frame 2 frame 3 frame 4 frame 5
* * spliQng event
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biotracks aims to be for cell tracking data what Bio-‐Formats is for imaging data
h5ps://commons.wikimedia.org/ h5p://www.openmicroscopy.org/site/products/bio-‐formats
naPve file format
naPve file format
naPve file format
your data, your analysis, your applicaPons…
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biotracks aims to be for cell tracking data what Bio-‐Formats is for imaging data
biotracks
h5ps://commons.wikimedia.org/ h5ps://assets.okfn.org/p/data/img/icon-‐512.png
naPve file format
your data, your analysis, your applicaPons…
biotracks integraPon with pandas enables analysis and visualizaPon rouPnes
Data: Marleen Van Troys, UGent
ImageJ/Fiji TrackMate DoG detector + LAP tracking 163 tracks
A common data format enables quick comparison of tracking algorithms
h5p://fiji.sc/samples/FakeTracks.Pf
ICY spot tracking plugin Spot detector + Mul5ple Hypothesis Tracking
ImageJ/Fiji TrackMate DoG detector + complex LAP tracking
A common data format enables quick comparison of tracking algorithms
ImageJ/Fiji TrackMate DoG detector + complex LAP tracking
ICY spot tracking plugin Spot detector + Mul5ple Hypothesis Tracking
h5p://fiji.sc/samples/FakeTracks.Pf
Standard data formats alone are not enough
Image credit: Ainsley Seago, PLoS Biology
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Minimum reporPng requirements and CVs improve data verificaPon and accessibility
ISA OME biotracks
Data deposi6on
MIACM
E
CV
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An open data ecosystem for cell migraPon research: what are the benefits?
• standardizaPon of data and metadata is essenPal for reproducibility and unambiguous interpretaPon of experiments
• data exchange = faster and easier access to results + quality control + integraPon with in silico modeling
• open data = opportuniPes for knowledge discovery, data mining, data re-‐use
• formulaPon of new hypotheses/principles
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CMSO needs community engagement
h5ps://cmso.science/cmso-‐workshop-‐in-‐essen-‐germany-‐19-‐and-‐20-‐june-‐2017/ h5ps://goo.gl/forms/eMs4m8YGZOmWOv0s1
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CMSO needs community engagement
h5ps://cmso.science/cmso-‐workshop-‐in-‐essen-‐germany-‐19-‐and-‐20-‐june-‐2017/ h5ps://goo.gl/forms/eMs4m8YGZOmWOv0s1
CC BY-‐SA 4.0
CC BY-‐SA 4.0
![Progress and Plans on Magnetic Reconnection for CMSO For NSF Site-Visit for CMSO May1-2, 2005 1. Experimental progress [M. Yamada] -Findings on two-fluid.](https://static.fdocuments.us/doc/165x107/5515184f55034673228b4d0f/progress-and-plans-on-magnetic-reconnection-for-cmso-for-nsf-site-visit-for-cmso-may1-2-2005-1-experimental-progress-m-yamada-findings-on-two-fluid.jpg)
