This document discusses the need for open data standards in cell migration research. It describes how standardizing data formats like biotracks for cell tracking data can facilitate data sharing and re-use. This would allow for more analysis possibilities and help establish best practices. The CMSO community is working to develop standards, including re-using some existing ones and defining new migration-specific standards. The ultimate goals are improved reproducibility, data verification and enabling new discoveries through data integration and mining.

1. TOWARDS OPEN DATA IN CELL
MIGRATION RESEARCH
@pcmasuzzo
paola.masuzzo@vib-ugent.be

2. CC BY-SA 4.0
60
STATISTICS SAY I HAVE
SECONDS
to capture your attention
https://de.wikipedia.org/wiki/Datei:Hourglass_2.svg, CC BY-SA 3.0

3. https://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

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Cell migration is involved in many processes
Masuzzo, PhD thesis, 2016

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Cell migration is involved in many processes
Masuzzo, PhD thesis, 2016

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Cells are able to move following many and
diverse strategies
Collective
migration
Multicellular
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
preparation
image
acquisition
image
processing
data
analysis
Servier Medical Art, CC-BY 3.0; Cell Image Library, CC-BY 3.0
An imaging-based cell migration
experimental workflow has diverse steps

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Servier Medical Art, CC-BY 3.0; Cell Image Library, CC-BY 3.0;
https://commons.wikimedia.org/
These steps produce rich data sets
represented in various file formats
sample
preparation
image
acquisition
image
processing
data
analysis

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Breaking down technical barriers means
facilitating data sharing
Image credit: Ainsley Seago, PLoS Biology

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Data sharing in turn means more analytical
possibilities
https://multimot.org/
Masuzzo, Trends in Cell Biology, 2015

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The first step towards data sharing is
standardization
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

17. CC BY-SA 4.0
Different information units require specific
standardization tasks
raw data &
metadata
set up experiment:
annotate
investigation,
study, assay
convert processed
and derived data
into standard
formats
process raw data
convert raw data &
metadata into
standard formats
analyze
data
experiment

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The ultimate goal is to enable data
re-analysis, re-use, re-purpose
raw data &
metadata
set up experiment:
annotate
investigation,
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

19. CC BY-SA 4.0
CMSO is a young community developing
standards for cell migration research
https://cmso.science/
https://github.com/CellMigStandOrg

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CMSO is a young community developing
standards for cell migration research
https://cmso.science/
https://github.com/CellMigStandOrg

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CMSO is re-using and adapting some of the
standards available in the community
ISA OME ?
http://isa-tools.org/
http://www.openmicroscopy.org/site
experimental
setup
imaging data and
metadata
analytical
results

22. CC BY-SA 4.0
And it is developing new standards for
cell migration-specific information
ISA OME biotracks
https://cellmigstandorg.github.io/Tracks/
https://github.com/CellMigStandOrg/biotracks
experimental
setup
imaging data and
metadata
analytical
results

23. 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

24. CC BY-SA 4.0
biotracks: tabular data packages
for cell tracking files
https://pypi.python.org/pypi/biotracks
https://github.com/CellMigStandOrg/biotracks
objects
links
tracks
segmentation
algorithm
linking
algorithm
connecting links
frame 1 frame 2 frame 3 frame 4 frame 5
** splitting event

25. CC BY-SA 4.0
biotracks: tabular data packages
for cell tracking files
objects
links
tracks
segmentation
algorithm
linking
algorithm
connecting links
frame 1 frame 2 frame 3 frame 4 frame 5
** splitting event

26. CC BY-SA 4.0
biotracks: tabular data packages
for cell tracking files
http://frictionlessdata.io/data-packages/
objects
links
tracks
segmentation
algorithm
linking
algorithm
connecting links
frame 1 frame 2 frame 3 frame 4 frame 5
** splitting event

27. CC BY-SA 4.0
biotracks aims to be for cell tracking data
what Bio-Formats is for imaging data
https://commons.wikimedia.org/
http://www.openmicroscopy.org/site/products/bio-formats
native file
format
native file
format
native file
format
your data, your
analysis, your
applications…

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biotracks aims to be for cell tracking data
what Bio-Formats is for imaging data
biotracks
https://commons.wikimedia.org/
https://assets.okfn.org/p/data/img/icon-512.png
native file
format
your data, your
analysis, your
applications…

29. biotracks integration with pandas enables
analysis and visualization routines
Data: Marleen Van Troys, UGent
ImageJ/Fiji TrackMate
DoG detector + LAP tracking
163 tracks

30. A common data format enables quick
comparison of tracking algorithms
http://fiji.sc/samples/FakeTracks.tif
ICY spot tracking plugin
Spot detector + Multiple Hypothesis Tracking
ImageJ/Fiji TrackMate
DoG detector + complex LAP tracking

31. A common data format enables quick
comparison of tracking algorithms
ImageJ/Fiji TrackMate
DoG detector + complex LAP tracking
ICY spot tracking plugin
Spot detector + Multiple Hypothesis Tracking
http://fiji.sc/samples/FakeTracks.tif

32. Standard data formats alone are not enough
Image credit: Ainsley Seago, PLoS Biology

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Minimum reporting requirements and CVs
improve data verification and accessibility
ISA OME biotracks
Data deposition
MIACME
CV

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An open data ecosystem for cell migration
research: what are the benefits?
• standardization of data and metadata is essential for
reproducibility and unambiguous interpretation of
experiments
• data exchange = faster and easier access to results
+ quality control
+ integration with in silico modeling
• open data = opportunities for knowledge discovery,
data mining, data re-use
• formulation of new hypotheses/principles

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CMSO needs community engagement
https://cmso.science/cmso-workshop-in-essen-germany-19-and-20-june-2017/
https://goo.gl/forms/eMs4m8YGZOmWOv0s1

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CMSO needs community engagement
https://cmso.science/cmso-workshop-in-essen-germany-19-and-20-june-2017/
https://goo.gl/forms/eMs4m8YGZOmWOv0s1

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