ArticleScientific reports2021
Automatic and unbiased segmentation and quantification of myofibers in skeletal muscle.
Article in Scientific reports, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 89 papers.
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Who cites it
89 citing papers in PubMed.
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- Structural determinants of quadriceps atrophy following ACL injury: Evidence for fibre atrophy without fibre loss or overt peripheral denervation.The Journal of physiology · 2026Article
- Transcriptomic Profiling Reveals Early Molecular Adaptations to Resistance Exercise During Disuse Muscle Atrophy with Complementary Automated H&E-Based Muscle Morphometry.Life (Basel, Switzerland) · 2026Article
- AP-1B Controls Several Levels of Cell Proliferation and Differentiation in Mouse Enteroids.Biology of the cell · 2026Article
- Resident mesenchymal progenitor cells require autocrine IGF-I in homeostatic and regenerating skeletal muscle.Stem cell reports · 2026Article
- Monocyte infiltration induces CNS arginine catabolism to fuel neuroinflammation.Nature immunology · 2026Article
- Aerobic exercise is associated with alleviation of skeletal muscle atrophy in CT26 tumor-bearing mice: insights from transcriptomic and weighted gene co-expression network analyses.BMC musculoskeletal disorders · 2026Article
- Concurrent jamming and mesenchymal-to-epithelial transitions during airway basal stem cell differentiation.iScience · 2026Article
- A novel machine-learning classification model detects oxidative fiber type transitions in a rabbit model of cerebral palsy.bioRxiv : the preprint server for biology · 2026Article
- Glassy dynamics in active epithelia emerge from an interplay of mechanochemical feedback and crowding.Nature communications · 2026Article
- FAP-intrinsic Hedgehog signaling controls intramuscular adipogenesis, fibrosis, and myofiber regeneration.bioRxiv : the preprint server for biology · 2026Article
- Intramuscular Adipose Tissue Accumulation is a Key Determinant of Limb Function in Peripheral Artery Disease.Circulation · 2026Article
- A Synovium-on-Chip Platform to Study Multicellular Interactions in Arthritis.Advanced healthcare materials · 2026Article
- Functional and structural pathologies in skeletal muscle of a rat model of Duchenne muscular dystrophy.Skeletal muscle · 2026Article
- Efficient in vivo targeting of the myocardial scar using Moloney murine leukaemia virus complexed with nanoparticles.The Journal of physiology · 2026Article
- Skeletal Muscle HSF1 Alleviates Age-Associated Sarcopenia and Mitochondrial Function Decline via SIRT3-PGC1α Axis.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Morphological and functional phenotyping of skeletal muscle and bone in the zQ175 knock-in mouse model of Huntington's disease.Journal of Huntington's disease · 2026Article
- FibroTrack: a standalone deep learning platform for automated fibrosis quantification in muscle and cardiac histology.Skeletal muscle · 2026Article
- Disease exacerbation in human DMD MYOrganoids enables gene therapy evaluation and unveils persistence of fibrotic activity.NPJ Regenerative medicine · 2026Article
29 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
Funding
Abstract
Skeletal muscle has the remarkable ability to regenerate. However, with age and disease muscle strength and function decline. Myofiber size, which is affected by injury and disease, is a critical measurement to assess muscle health. Here, we test and apply Cellpose, a recently developed deep learning algorithm, to automatically segment myofibers within murine skeletal muscle. We first show that tissue fixation is necessary to preserve cellular structures such as primary cilia, small cellular antennae, and adipocyte lipid droplets. However, fixation generates heterogeneous myofiber labeling, which impedes intensity-based segmentation. We demonstrate that Cellpose efficiently delineates thousands of individual myofibers outlined by a variety of markers, even within fixed tissue with highly uneven myofiber staining. We created a novel ImageJ plugin (LabelsToRois) that allows processing of multiple Cellpose segmentation images in batch. The plugin also contains a semi-automatic erosion function to correct for the area bias introduced by the different stainings, thereby identifying myofibers as accurately as human experts. We successfully applied our segmentation pipeline to uncover myofiber regeneration differences between two different muscle injury models, cardiotoxin and glycerol. Thus, Cellpose combined with LabelsToRois allows for fast, unbiased, and reproducible myofiber quantification for a variety of staining and fixation conditions.
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