cell migration open data and open science

AN OPEN DATA EXCHANGEFOR CELL MIGRATION RESEARCH

paola masuzzo

@pcmasuzzo

[email protected] omics and systems biology groupVIB / Ghent University, Ghent, Belgium

CC BY-SA 4.0

MULTIMOT: towards global exchangeof cell migration data

CellMissy: a ‘little but fierce’ softwarefor cell migration data

Open science: why you should speak itand how to learn it

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Cell migration is necessary for many physiological conditions

Masuzzo, PhD thesis, 2016

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Unfortunately, it is also implicated in many diseases, such as metastatic cancer

Masuzzo, PhD thesis, 2016

CC BY-SA 4.0

A typical experimental workflow for a cell migration study is composed of diverse steps

Servier Medical Art, CC-BY 3.0; Cell Image Library, CC-BY 3.0

sample preparation

image acquisition

image processing

data analysis

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High-throughput experimentsproduce complex and rich data sets

sample preparation

image acquisition

image processing

data analysis

• paper laboratory notebooks

• electronic laboratory notebooks

• spreadsheets• text files• protocols• papers...

• raw files• XML files• proprietary

microscope or acquisition software files ND2 for Nikon, LIF for Leica, OIB or OIF for Olympus, LSM or ZVI for Zeiss

• image files with pixel values and metadata

• png, jpeg, tiff, avi• text files

describing processing algorithms

• text files describing extracted features

• graphs, plots• analysis pipelines• text files

describing computational algorithms...

Servier Medical Art, CC-BY 3.0; Cell Image Library, CC-BY 3.0

CC BY-SA 4.0

CellMissy is our open-source tool for cell migration data management and analysis

https://github.com/compomics/cellmissyMasuzzo, Bioinformatics, 2013

https://github.com/compomics/cellmissy


CC BY-SA 4.0


https://github.com/compomics/cellmissy Masuzzo, Bioinformatics, 2013



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CellMissy guides and captures the experimental setup

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This experimental setup encloses detailed metadata annotation

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CellMissy can automatically import all the data and metadata

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All the data are then stored in a structured way in a relational database

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Cell migration can occur in both collective and individual fashion

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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CellMissy enables efficient collective cell migration data exploration and analysis

time (min)

Area

()

wound areacell-covered area

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A primary focus of data analysis is statistical comparison of samples

analysis report with graphs,tables and results

cell sheet velocity (µm²/min)

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Many informative parameters can be derived from single-cell trajectories

x

ysingle cell

Masuzzo, 2017, under revision

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ࢻ

Euclideandistance

Cumulativedistance

x

ysingle cell


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ࢻ

Euclideandistance

Cumulativedistance

x

ysingle cell parameter mathematical description

di: instantaneous displacement of the cell centroid between adjacent time points

si: instantaneous speed between adjacent time points

αi: turning angle between consecutive steps

dtot: cumulative distance, total distance travelled

dnet: Euclidean distance, net distance travelled

ep_dr: end-point directionality ratio (confinement ratio, meandering index)

MD: median displacement

MS: median speed

MTA: median turning angle


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Step-centric parameters are aggregated values of all migration steps

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Trajectory-centric parameters are instead computed on each cell and then averaged for the cell population

...

trajectory 1

trajectory 2

trajectory 3

trajectory 4

trajectory 5

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The new single-cell module allows for both these computations to take place

...

trajectory 1

trajectory 2

trajectory 3

trajectory 4

trajectory 5

trajectory-centric parameters

trajectory displacement (µm)

dens

ity

step displacement (µm)

dens

ity

pool of migration steps

step-centric parameters


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A flexible two-step filtering criterion is implemented for data quality control


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Data and metadata exchange options are already available in CellMissy

lab A

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lab A lab B

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lab B

This is one file in CellMissy! (≈10 MB)

lab A

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But we can easily extend this conceptto a bigger scale

DataRepository Local Software

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MULTIMOT is creating an open cell migration data exchange ecosystem

https://multimot.org/ Masuzzo, Trends in Cell Biology, 2016

https://multimot.org/

https://multimot.org/

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MULTIMOT is creating an open cell migration data exchange ecosystem

https://cmso.science/Masuzzo, Trends in Cell Biology, 2016

https://cmso.science/

https://cmso.science/

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This open data ecosystem falls into the broader context of open science

Knoth and Pontika, Open Science Taxonomy, figshare, 2015

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There are four widely recognized thematic pillars of open science

Masuzzo, PeerJ Preprints, 2017https://doi.org/10.7287/peerj.preprints.2689v1

https://doi.org/10.7287/peerj.preprints.2689v1



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OPEN SCIENCE

DATA

CODE

PAPERS

REVIEW

> OPEN DATA




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Open data means freedom to access, use and re-use for any purpose

http://opendefinition.org/od/



CC BY-SA 4.0

Open data means freedom to access, use and re-use for any purpose

There are many open knowledge definition conformant licenses

CC0 waiverhttps://creativecommons.org/publicdomain/zero/1.0/

CC BY (Attribution only)https://creativecommons.org/licenses/by/4.0/

CC BY-SA (Attribution ShareAlike)https://creativecommons.org/licenses/by-sa/4.0/

http://opendefinition.org/od/, http://opendefinition.org/licenses

https://creativecommons.org/publicdomain/zero/1.0/



https://creativecommons.org/licenses/by/4.0/



https://creativecommons.org/licenses/by-sa/4.0/






http://opendefinition.org/licenses/

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A lot of repositories are available to upload research materials and data

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You certainly don’t need to know more than 1,500 repositories by heart

https://biosharing.org/databases/



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OPEN SCIENCE

DATA

CODE

PAPERS

REVIEW

> OPEN ACCESS




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The impacts of open access are very broad and affect many areas

Tennant, Masuzzo, F1000Research, 2016Wikimedia Commons, Public Domain

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Publish your work open access can bring you enormous benefits

CC-BY Danny Kingsley & Sarah Brown

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Do you want to engage with Open Science?

When possible, use and cite existing public data

Whenever feasible, share your research data through trusted repositories. General-purpose repositories and domain-specific ones

are available on the web. Make sure you share metadata as well

If you use software code as part of your research cycle, release the code. Specify the open source license you intend to use, and link the

readers to a stable repository that hosts the code

Post free copies of your research articles online. Most journals allow this, sometimes after an embargo period of 6-12 months

Post preprints of your research manuscripts online, ideally at the same time of official submission to a journal

When possible, choose an open access journal as venue for your scientific articles. Keep in mind that subscription journals also offer an

open access solution, upon payment of extra fees





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www.compomics.com@compomics