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Mayeuf-Louchart A, Hardy D, Thorel Q, Roux P, Gueniot L, Briand D, Mazeraud A, Bouglé A, Shorte SL, Staels B, Chrétien F, Duez H, Danckaert A. MuscleJ: a high-content analysis method to study skeletal muscle with a new Fiji tool. Skelet Muscle 2018; 8:25. [PMID: 30081940 PMCID: PMC6091189 DOI: 10.1186/s13395-018-0171-0] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 07/20/2018] [Indexed: 11/22/2022] Open
Abstract
Background Skeletal muscle has the capacity to adapt to environmental changes and regenerate upon injury. To study these processes, most experimental methods use quantification of parameters obtained from images of immunostained skeletal muscle. Muscle cross-sectional area, fiber typing, localization of nuclei within the muscle fiber, the number of vessels, and fiber-associated stem cells are used to assess muscle physiology. Manual quantification of these parameters is time consuming and only poorly reproducible. While current state-of-the-art software tools are unable to analyze all these parameters simultaneously, we have developed MuscleJ, a new bioinformatics tool to do so. Methods Running on the popular open source Fiji software platform, MuscleJ simultaneously analyzes parameters from immunofluorescent staining, imaged by different acquisition systems in a completely automated manner. Results After segmentation of muscle fibers, up to three other channels can be analyzed simultaneously. Dialog boxes make MuscleJ easy-to-use for biologists. In addition, we have implemented color in situ cartographies of results, allowing the user to directly visualize results on reconstituted muscle sections. Conclusion We report here that MuscleJ results were comparable to manual observations made by five experts. MuscleJ markedly enhances statistical analysis by allowing reliable comparison of skeletal muscle physiology-pathology results obtained from different laboratories using different acquisition systems. Providing fast robust multi-parameter analyses of skeletal muscle physiology-pathology, MuscleJ is available as a free tool for the skeletal muscle community. Electronic supplementary material The online version of this article (10.1186/s13395-018-0171-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alicia Mayeuf-Louchart
- Inserm, CHU Lille, Institut Pasteur de Lille, University of Lille, U1011 - EGID, 1 rue du Pr. Calmette, F-59000, Lille, France.
| | - David Hardy
- Experimental Neuropathology Unit, Infection and Epidemiology Department, Institut Pasteur, 25, rue du Docteur Roux, 75015, Paris, France
| | - Quentin Thorel
- Inserm, CHU Lille, Institut Pasteur de Lille, University of Lille, U1011 - EGID, 1 rue du Pr. Calmette, F-59000, Lille, France
| | - Pascal Roux
- UTechS PBI (Imagopole)-Citech, Institut Pasteur, 25, rue du Docteur Roux, 75015, Paris, France
| | - Lorna Gueniot
- Experimental Neuropathology Unit, Infection and Epidemiology Department, Institut Pasteur, 25, rue du Docteur Roux, 75015, Paris, France
| | - David Briand
- Experimental Neuropathology Unit, Infection and Epidemiology Department, Institut Pasteur, 25, rue du Docteur Roux, 75015, Paris, France
| | - Aurélien Mazeraud
- Experimental Neuropathology Unit, Infection and Epidemiology Department, Institut Pasteur, 25, rue du Docteur Roux, 75015, Paris, France
| | - Adrien Bouglé
- Experimental Neuropathology Unit, Infection and Epidemiology Department, Institut Pasteur, 25, rue du Docteur Roux, 75015, Paris, France
| | - Spencer L Shorte
- UTechS PBI (Imagopole)-Citech, Institut Pasteur, 25, rue du Docteur Roux, 75015, Paris, France
| | - Bart Staels
- Inserm, CHU Lille, Institut Pasteur de Lille, University of Lille, U1011 - EGID, 1 rue du Pr. Calmette, F-59000, Lille, France
| | - Fabrice Chrétien
- Experimental Neuropathology Unit, Infection and Epidemiology Department, Institut Pasteur, 25, rue du Docteur Roux, 75015, Paris, France
| | - Hélène Duez
- Inserm, CHU Lille, Institut Pasteur de Lille, University of Lille, U1011 - EGID, 1 rue du Pr. Calmette, F-59000, Lille, France
| | - Anne Danckaert
- Experimental Neuropathology Unit, Infection and Epidemiology Department, Institut Pasteur, 25, rue du Docteur Roux, 75015, Paris, France. .,UTechS PBI (Imagopole)-Citech, Institut Pasteur, 25, rue du Docteur Roux, 75015, Paris, France.
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