MethodsJ2: a software tool to capture metadata and generate comprehensive microscopy methods text
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FOCUS | correspondence
FOCUS | correspondence
MethodsJ2: a software tool to capture metadata
and generate comprehensive microscopy
methods text
To the Editor — Proper reporting of
metadata is essential to reproduce 1 Create a Micro-Meta App microscope.JSON file. Hardware metadata
microscopy experiments, interpret results
and share images1,2. The lack of methods
reporting in microscopy is evident in that 2 Download MethodsJ2 script. Install Fiji/ImageJ if needed.
few research articles pass a test for the
minimal information required to reproduce
experiments1 (about 17% of 240 articles
3 Run the MethodsJ2 script.
containing 1,500 figures with images).
The problem is compounded by the number
and variety of microscope modalities, Open the microscope image and select a Microscope.JSON
Image metadata
options and associated components. 4
hardware configuration file. OMERO OME TIFF metadata
Automation has distanced researchers
from the technical parameters, so it can be
difficult for them to know what information 5
The user is guided... through selection of hardware and
settings information.
Guided by imaging scientist
needs to be reported. MethodsJ2 is an
ImageJ/Fiji-based software tool that aims to
improve reproducibility in microscopy Draft imaging methods section text is generated. Text should
by capturing image metadata from be reviewed and modified as needed.
multiple sources, consolidating it and 6
automatically generating methods text Automated generation of microscopy platform
for publication. acknowledgement.
Research resource ID
To properly evaluate and reproduce
microscopy images, information about
sample preparation, experimental Fig. 1 | MethodsJ2 workflow overview. Steps required to automatically generate microscopy methods
conditions, microscope hardware, image text. Image metadata are collected from the microscope image acquisition software metadata in
acquisition settings and image analysis the image file using the OME TIFF tools. Hardware metadata are collected from a Micro-Meta App
parameters is required. This information is Microscope.JSON file.
called metadata and is defined as ‘a set of
data that describes and gives information
about other data’. Researchers involved in education around microscopy metadata facility impact, acknowledgement text,
the 4D Nucleome initiative3 and Bioimaging and straightforward accessible tools are including a facility Research Resource ID
North America (BINA) (https://www. vital for successful implementation of such (RRID, https://scicrunch.org/resources) can
bioimagingna.org/) have developed guidelines. MethodsJ2 is an extensible, be added to the script. The methods text is
extensive community-driven specifications open-source microscopy methods reporting then automatically generated but must be
for microscopy metadata4,5. These software tool that runs in ImageJ/Fiji and reviewed and edited.
specifications build on a previous Open builds on MethodsJ1,13,14. Integration with Comprehensive methods reporting
Microscopy Environment (OME) model6 ImageJ/Fiji should make it broadly available is essential for reporting imaging data,
and include an in-depth community-driven to experimental scientists. sharing images and emerging new
microscopy metadata model for light MethodsJ2 automatically gathers methods16–22. Progress along the path
microscopy called 4DN-BINA-OME4. The metadata from the image using OME of rigor and reproducibility is essential
model scales with experimental design, BioFormats (for example, pixel size, for high quality microscope-based
instrument complexity and the degree to magnification) and captures microscopy science and is a shared responsibility.
which image processing and quantitative metadata from a Microscope.JSON file Experimental scientists must use due
image analysis are required for interpreting generated using Micro-Meta App5,15. diligence to understand the fundamentals
results. This ensures that essential Micro-Meta App is a companion software of the technologies and required
information is included while minimizing tool that guides researchers step-by-step in microscope metadata on which their
the burden on experimental scientists to the collection of community-standardized research relies. Imaging scientists need
collect and report metadata7. microscopy metadata for a specific to educate experimental scientists, so
Microscope metadata guidelines8–10, microscope4. MethodsJ2 also guides the that they understand what metadata
examples of what can go wrong if metadata user to enter specific experimental and need to be reported and why. Microscope
are not reported11 and descriptions of the sample metadata (for example, cell type, manufacturers ought to integrate, automate
importance of measuring and reporting dyes). Finally, the software guides the user and report microscope metadata. Scientific
microscope quality control12 have been through a step-by-step validation of the publishers and reviewers have a duty to
published. Increased awareness and metadata. To improve tracking of imaging promote community-based guidelines4,6,23
Nature Methods | www.nature.com/naturemethodscorrespondence | FOCUS
correspondence | FOCUS
and to ensure that published microscope 6. Click ‘OK’. Draft methods text and any Carolina, Chapel Hill, NC, USA. 9UNC Neuroscience
images meet a minimum standard. Funding custom facility acknowledgment state- Center, University of North Carolina, Chapel Hill,
agencies need to uphold high-quality ment are automatically generated and NC, USA. 10Light Microscopy Core Facility, Duke
reproducible microscope images and ensure appear in a popup window, are copied to University, Durham, NC, USA. 11University Imaging
that detailed microscope metadata are the clipboard and can be pasted Centers, University of Minnesota, Minneapolis, MN,
available when images are publicly shared. into a manuscript. A.csv file of the micro- USA. 12Department of Neuroscience, University of
MethodsJ2 and two companion software scope metadata is generated and saved Minnesota, Minneapolis, MN, USA.
tools — Micro-Meta App15 and OMERO. (see the sample.csv file in the Supple- ✉e-mail: claire.brown@mcgill.ca
mde23 — advance rigor and reproducibility mentary Information and on the GitHub
in microscopy (Supplementary Fig. 1), portal). Note: it is the responsibility of the Published: xx xx xxxx
but there are still challenges. Microscopy experimental scientists to review the draft https://doi.org/10.1038/s41592-021-01290-5
metadata are often limited, not in standard text and ensure that it is accurate.
formats, not accessible owing to the use References
1. Marques, G., Pengo, T. & Sanders, M. A. eLife 9, e55133
of proprietary microscope manufacturer (2020).
software and/or lost when images are Reporting summary 2. Lee, J. Y. & Kitaoka, M. Mol. Biol. Cell 29, 1519–1525
saved and opened with third-party Further information on research design is (2018).
software4. Microscope manufacturers available in the Nature Research Reporting 3. Dekker, J. et al. Nature 549, 219–226 (2017).
4. Hammer, M. et al. Nat. Methods Preprint at bioRxiv https://doi.
need to work with the global community Summary linked to this article. org/10.1101/2021.04.25.441198 (2021).
through organizations such as Quality 5. Rigano, A. et al. 4DN-BINA-OME (NBO) Tiered Microscopy
Metadata Specifications v2.01 https://github.com/WU-BIMAC
Assessment and Reproducibility for Online content (2021).
Instruments & Images in Light Microscopy Any methods, additional references, Nature 6. Goldberg, I. G. et al. Genome Biol. 6, R47 (2005).
(QUAREP-LiMi)24,25 to automate the Research reporting summaries, source data,
7. Huisman, M. et al. Preprint at ArXiv https://arxiv.org/
abs/1910.11370 (2021).
collection of metadata, ensure they extended data, supplementary information, 8. Aaron, J. S. & Chew, T.-L. J. Cell Sci. 134, jcs254151
conform to community standards4,6,23 acknowledgements, peer review (2021).
and make them readily available. information; details of author contributions 9. Linkert, M. et al. J. Cell Biol. 189, 777–782 (2010).
10. Heddleston, J. M., Aaron, J. S., Khuon, S. & Chew, T. -L. J. Cell Sci.
The implementation and evolution and competing interests; and statements of 134, jcs254144 (2021).
of MethodsJ2, Micro-Meta App15 and data and code availability are available at 11. Montero Llopis, P. et al. Nat. Methods https://doi.org/10.1038/
OMERO.mde23, will promote transparency https://doi.org/10.1038/s41592-021-01290-5. s41592-021-01156-w (2021).
12. Nelson, G., Gelman, L., Faklaris, O., Nitschke, R. & Laude, A.
and reproducibility and help stakeholders Preprint at arXiv https://arxiv.org/abs/2011.08713 (2020).
to ensure that microscopy metadata are 13. Ryan, J. et al. Preprint at bioRxiv https://doi.
documented and reported. Data availability org/10.1101/2021.06.23.449674 (2021).
14. Ryan, J. et al. https://doi.org/10.5281/zenodo.5172827
The following list describes the Data in the form of a sample image and (2021).
MethodsJ2 workflow (summarized in Fig. 1); Microscope.JSON file are available at https:// 15. Rigano, A. et al. Nat. Methods Preprint at bioRxiv https://doi.
a more detailed workflow and sample github.com/ABIF-McGill/MethodsJ2. org/10.1101/2021.05.31.446382 (2021).
microscope metadata are available in the 16. Ellenberg, J. et al. Nat. Methods 15, 849–854
(2018).
Supplementary Information. 17. Miyakawa, T. Mol. Brain 13, 24 (2020).
Code availability 18. Sansone, S. A. et al. Nat. Biotechnol. 37, 358–367
1. Use Micro-Meta App to create and save Full source code and step-by-step (2019).
19. Botvinik-Nezer, R. et al. Nature 582, 84–88 (2020).
a Microscope.JSON file. Give compo- instructions are available at https://github. 20. Sheen, M. R. et al. Replication study: biomechanical remodeling
nents detailed names, as this text popu- com/ABIF-McGill/MethodsJ2 and https:// of the microenvironment by stromal caveolin-1 favors tumor
lates the methods text. For example, put doi.org/10.5281/zenodo.5172827. ❐ invasion and metastasis. Elife 8, e4512 (2019).
21. Gosselin, R. D. BioEssays 42, e1900189 (2020).
‘63×/1.4 NA Plan-Apochromatic oil 22. Gibney, E. Nature 577, 14 (2020).
immersion’ rather than ‘63×’. Joel Ryan 1,2, Thomas Pengo 3, 23. Kunis, S., Hänsch, S., Schmidt, C., Wong, F. & Weidtkamp-Peters,
2. Download the MethodsJ2 script (file Alex Rigano4, Paula Montero Llopis 5
, S. Nat. Methods Preprint at arXiv https://arxiv.org/abs/2103.02942
(2021).
named: MethodsJ2_v1_2_.py), an ex- Michelle S. Itano 6,7,8,9, 24. Boehm, U. et al. Nat. Methods https://doi.org/10.1038/s41592-
ample Microscope.JSON file and an ex- Lisa A. Cameron 10, 021-01162-y (2021).
ample image file from GitHub (https:// Guillermo Marqués 11,12, 25. Nelson, G. et al. J. Microsc. 284, 56–73 (2021).
github.com/ABIF-McGill/MethodsJ2). Caterina Strambio-De-Castillia 4,
Download and install ImageJ/Fiji Mark A. Sanders 11,12 and Acknowledgements
(https://fiji.sc/). Claire M. Brown 1,2 ✉ We thank our microscopy core facility staff and users of
3. Drag the MethodsJ2 script file and drop 1
Advanced BioImaging Facility (ABIF), McGill McGill University Advanced BioImaging Facility (ABIF)
it onto the ImageJ/Fiji toolbar. The University, Montreal, Quebec, Canada. 2Department (RRID: SCR_017697), University Imaging Centers of
the University of Minnesota (RRID: SCR_020997),
script editor will open, then press ‘Run’. of Physiology, McGill University, Montreal, Quebec, MicRoN (Microscopy Resources on the North Quad)
4. Select an image file. The image metadata Canada. 3University of Minnesota Informatics Core at Harvard Medical School, UNC Neuroscience
are automatically extracted. Sample Institute, University of Minnesota, Minneapolis, Microscopy Core (RRID: SCR_019060) (supported,
information can be added manually. MN, USA. 4Program in Molecular Medicine, in part, by NIH-NINDS Neuroscience Center Support
Grant P30 NS045892 and NIH-NICHD Intellectual and
Select a Microscope.JSON file for the University of Massachusetts Chan Medical School,
Developmental Disabilities Research Center Support
corresponding microscope. Worcester, MA, USA. 5MicRoN, Department of Grant P50 HD103573) and Duke University Light
5. Follow the step-by-step guidance to Microbiology, Harvard Medical School, Boston, MA, Microscopy Core Facility. Chan Zuckerberg Initiative
validate the metadata and input critical USA. 6Neuroscience Microscopy Core, University of DAF, an advised fund of Silicon Valley Community
hardware and settings information. North Carolina, Chapel Hill, NC, USA. 7Department Foundation, supports C.M.B. (grant no. 2020-225398),
C.S.-D.-C. (grant no. 2019-198155 (5022)) and M.S.I.
Note: have an experienced microscope of Cell Biology & Physiology, University of North
(grant no. 2019-198107). We also acknowledge NIH
user or imaging scientist help with Carolina, Chapel Hill, NC, USA. 8Carolina Institute grants 2U01CA200059-06 and 1U01EB021238 to
this step. for Developmental Disabilities, University of North C.S.-D.-C.
Nature Methods | www.nature.com/naturemethodsFOCUS | correspondence
| FOCUS correspondence
Author contributions conceptualization, validation, writing review and Additional information
J.R.: conceptualization, software development, editing. G.M.: conceptualization, validation. C.S.-D.-C.: Supplementary information The online version
validation, data curation, writing review and conceptualization, software, validation, supervision, contains supplementary material available at https://doi.
editing. T.P.: conceptualization, software development, funding acquisition. M.A.S.: conceptualization, org/10.1038/s41592-021-01290-5.
validation. A.R.: conceptualization, software writing review and editing. C.M.B.: conceptualization, Peer review information Nature Methods thanks Jon
development, validation. P.M.L.: conceptualization, validation, writing original draft, writing review and Mulholland, Brian Slaughter and the other, anonymous,
validation, writing review and editing. editing, supervision, project administration, funding reviewer(s) for their contribution to the peer review of
M.S.I.: conceptualization, validation. L.A.C.: acquisition. this work.
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