Minimal reporting requirements for cell migration - update from Working Group 1 of the Cell Migration Standardisation Organisation

1. Minimal reporting
requirements for
cell migration (WG1)
Alejandra Gonzalez-Beltran
Oxford e-Research Centre, University of Oxford
@alegonbel
CSMO Workshop, 19th June 2017, Essen, Germany

2. Working Group Objectives
● Formulation of a reporting guideline for Cell Migration experiments
(MIACME) supporting the requirements to make data produced in such
experiments FAIR (Findable Accessible Interoperable and Reusable)
● Reach agreement from the community on the minimal descriptors (and
extended descriptors) required to understand, interpret, evaluate, replicate
and disseminate cell migration experiments
● Use MIACME to promote data access, data discovery, data preservation
and to maximise data re-use and repurpose through efficient annotation for
long term archiving
● Ultimately, enable reproducibility of cell migration experiments

3. MIACME development
● Gradient of information (data discovery/access/preservation to understand,
interpret, evaluate, re-use, repurpose, replicate, reproduce)
● Iterative process: (design → test → refine → evaluate) cycle
● “Minimal” set of descriptors
○ Strike the right balance between number of descriptors and the objectives for collecting them
○ “Minimal” is dependent on experiment type
■ Consider core set of descriptors and extensions, if necessary
○ “Optimal” set of descriptors
● Community-led process
○ Community consensus is key to agree on a standard way of reporting cell migration
experiments

4. https://github.com/CellMigStandOrg/MIACME

5. Community-driven development
http://cellmigstandorg.github.io/MIACME/v0.2/spec/

6. MIACME development - timeline
● Pre-inaugural workshop compilation of material
● 1st CMSO workshop
○ Raking of descriptors
○ MIACME survey
● MIACME v0.1 - (released January 2017)
● 2nd CMSO workshop
○ Revised MIACME v0.1, simplification: selected minimal descriptors
○ Evaluation through the representation of experiments
● MIACME v0.2 (ready for release)

7. https://biosharing.org/collection/MIBBI

8. MIACME
available in
Biosharing
portal of
standards
(and related
Standards,
Databases
and Policies)
https://biosharing.org/bsg-s000642

9. MIACME Survey
to identify and rank
possible MIACME
descriptors
http://tiny.cc/miacme-survey

10. MIACME Descriptors Ranking
http://tiny.cc/miacme-ranking

11. MIACME v0.1 http://tiny.cc/miacme-0-1-fig

12. MIACME v0.1 list of descriptors
Focused on in vitro experiments
http://tiny.cc/miacme-live

13. MIACME v0.1 Specification
http://cellmigstandorg.github.io/MIACME/v0.1/spec/

14. MIACME v0.2 - Experimental setup
Assay
type
Interference
Microenv
substrate
Microenv
tissue Cell type Medium
Experimental setup
single-cell
migration,
collective cell
migration,
developmental
assay, immune
response,
chemotaxic,
microfluidic,
wound-healing,
spheroid
RNAi, gene
construct,
chemicals, serum,
substrate
stiffness
-------------------------
specific protein
glass, plastic,
ECM, gel
-------------------------
Collagen,
fibronectin
mouse,
dermis,
Zebrafish
embryo
cell line,
primary cell,
endogenous
cell
EGF, HGF
one or the other

15. MIACME v0.2 - Imaging condition
Imaging condition
Imaging
modality
confocal
microscopy,
spinning disk,
wide-field,
multi-photon,
light-sheet,
super-resolution,
phase-contrast
Temporal
resolution
end-point,
time-lapse
Duration and
frequency
Objective
Channel
readout 1..n
36 hours, 10
minutes
20x, oil
conditional on
time-lapse
Specific
protein/subcellular
compartment,
traction force
beads, ratio (FRET),
cell body/bodies
-----------------------------
-
antibody,
FP-tagged, dye

16. MIACME v0.2 - Data
Data (1..n)
Raw images
YES or NO
Total number
of images
conditional
on YES
250
Processed
images
Extracted
features
trajectories (x, y, t),
derived quantities
like cell speed,
persistence of
motion, shape
features (cell area,
cell solidity, cell
perimeter…)
filtered images,
deconvoluted
images, masked
images, images
with tracks overlay,
traction flow, PIV
flow fields

17. MIACME v0.2

23. Roadmap
MIACME v0.2 has focused on identifying the main descriptors. In the next steps,
we will:
● produce more examples of MIACME-compliant descriptions of different types
of cell migration experiments for evaluation
● include further requirements related to semantic artifacts and other external
resources
● consider relationship/alignment with other resources, e.g. MIACA - Minimum
Information About a Cellular Assay
● release new versions of the MIACME checklist after incorporating the
feedback received

24. Workshop Work Plan Proposal
● Revision of MIACME v0.2
○ Provide comments on current descriptors and suggestions for additions / modifications
○ Has the simplification reached the right balance?
● Collect publications/experiments/datasets to be described with MIACME
○ Work in on own publication/dataset
○ Peer assessment
● Analysis of groups’ experimental setups
● Create task forces to deal with specific experiment types
● Work on automatic extraction of some MIACME metadata
○ e.g. objective and temporal resolution
● Interactions with other working groups to consider MIACME in relation to
○ Semantic artifacts and other external resources
○ Formats and APIs

25. Acknowledgements
Paola Masuzzo
Marleen van Troys
Philippe Rocca-Serra
All Working Group 1 members

26. Thank you!
Questions?