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Data availability
We have built a web interface (https://www.emitometrix.org) where all documents are centralized: from the containerized applications (Windows, Linux, MacOS) to a ‘Try it Yourself’ demo) to a detailed instruction manual (.pdf), video tutorials (.mp4) and FAQ sections. Images used for training and testing the models are available from the corresponding authors on request.
Code availability
The different versions of the software (Linux: https://doi.org/10.5281/zenodo.17049894, Windows: https://doi.org/10.5281/zenodo.17049893 and macOS: https://doi.org/10.5281/zenodo.17049887) and the documentation for the EMito-Metrix tool are available at https://github.com/Restore-Lab/EMitoMetrix.
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Acknowledgements
We thank all members of the mouse core facilities (UMS006, ANEXPLO, INSERM, Toulouse), in particular C. Simondon, É. Sinhlivong and C. Baudelin for their support and technical assistance. This study is supported by grants from INSERM, Paul Sabatier University, CNRS, EFS, the French National Research Agency (ANR-21-CE14-0054-02) and the INSERM TRANSFERT (COPOC 2025 U1301 TLS – eMitoMETRIX). The IHU HealthAge was supported by the French National Research Agency as part of the France 2030 programme (reference number: ANR 23 IAHU 0011). This work was supported by the INSPIRE programme, grants from the Region Occitanie, France (reference number: 1901175), Fondation pour la Recherche Médicale (DEQ20180339226), the Programme d’investissements d’avenir and the French National Research Agency for the national infrastructure ‘ECELLFrance: development of mesenchymal stem cell-based therapies’ (PIA-ANR-11-INBS-005). We acknowledge the CMEAB imaging facility, a member of the national infrastructure France-BioImaging supported by the French National Research Agency (ANR-10-INBS-04). The METi imaging facility and RESTORE data analysis facility (Genotoul-TRI) member of France-BioImaging is supported by the French National Research Agency (ANR-24-INBS-0005 FBI BIOGEN). G.G. is supported by a grant from the Natural Sciences and Engineering Council of Canada (NSERC; RGPIN-2021-03724) and by a Chercheur-boursier junior 2 salary award from the Fonds de recherche du Québec en Santé (FRQS-297877). G.G. and S.N.A.H. are supported by a grant from the Canadian Institutes of Health Research (CIHR; MOV-438450). E.D. and G.G. received a grant from the Centre d’Excellence en Recherche sur les Maladies Orphelines–Fondation Courtois (CERMO-FC). E.D. is also supported by a Chercheur-boursier junior 2 salary award from the Fonds de recherche du Québec en Santé (FRQS-31186). L. Formentini is supported by Fundación Ramon Areces and PID2022-136738OB-I00 (MCIN/AEI/10.13039/501100011033). B.S.A. receives support from FPU predoctoral fellowship (FPU2022/00218). A. Mourier is supported by a grant from the French National Research Agency (ANR-22-CE14-0040). O.R.B. is supported by a grant from the French National Research Agency (ANR-20-CE92-0020). E.M. is supported by a grant from the French National Research Agency (ANR-21-CE14-0054-02). E.D. is supported by a grant from the French National Research Agency (EUR CARe N°ANR-18-EURE-0003). A.Q. was supported by the INSPIRE programme, grants from the Region Occitanie, France (reference number: 1901175) and from the French National Research Agency (ANR-21-CE14-0054-02). J.N. is supported by the INCA (PLBIO 2020-010, DIALAML).
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Contributions
E.M. designed the research, organized sample collections, performed experiments, analysed data and wrote and edited the manuscript. E.D. designed the research and methodology, analysed data and wrote and edited the manuscript. L.M.H. generated and provided human electron microscopy pictures and reviewed and commented on the manuscript. A.Q., S.E. and J.N. performed experiments and analysed data from fish and mice and reviewed and commented on the manuscript. D.G., B.P., V.S. and S.B. performed tissue processing and electron microscopy. C.S. and L.D. performed experiments, analysed data from Fly and revised and commented on the manuscript. A. Mattout performed revisions and commented on the manuscript. V.P. and L.C. have provided help to design new imaging analysis and reviewed and commented on the manuscript. J.R., A.Y., P.V. and C.D. have provided daily support, fruitful discussions, fundings and revised and commented on the manuscript. L. Ferrucci provided human electron microscopy pictures and reviewed and commented on the manuscript. J.-P.L.-G., S.N.A.H., E.D. and G.G. have provided electron microscopy pictures of human and mouse skeletal muscles displaying mitochondrial dysfunctions, helped to fine-tune the application and revised and commented on the manuscript. L. Formentini and B.S.A. have provided electron microscopy pictures of mouse models of mitochondrial dysfunction, helped to fine-tune the application and revised and commented on the manuscript. A. Mourier and O.R.B. provided electron microscopy pictures and/or tissue samples from mouse models of mitochondrial dysfunction and revised and commented on the manuscript. H.P. has containerized the application, designed, built and run the online demo and designed and built the web interface. J.A. and P.M. designed metrics to evaluate mitochondrial ultrastructure, supervised the data computation and analysis and revised and commented on the manuscript. M.V. conceived the EMitoMetrix tool, designed all experiments, analysed data, wrote the manuscript and supervised the project. J.-P.P. conceived the original hypothesis, designed all experiments, analysed data, wrote the manuscript, provided fundings and supervised the project.
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Morin, E., Doumard, E., Hartnell, L.M. et al. EMito-Metrix enables automated evaluation of mitochondrial morphology across species. Nat Metab (2025). https://doi.org/10.1038/s42255-025-01400-z
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DOI: https://doi.org/10.1038/s42255-025-01400-z
