Additional file 1 of MuscleJ2: a rebuilding of MuscleJ with new features for high-content analysis of skeletal muscle immunofluorescence slides
Creators: name: Danckaert, Anne
name: Trignol, Aurélie
name: Le Loher, Guillaume
name: Loubens, Sébastien
name: Staels, Bart
name: Duez, Hélène
name: Shorte, Spencer L.
name: Mayeuf-Louchart, Alicia
Publisher: name: figshare
Year: 2023
Subjects: subject: Space Science
subject: Physiology
subject: FOS: Biological sciences
subject: Biological Sciences not elsewhere classified
subject: Information Systems not elsewhere classified

description: Additional file 1: Fig. S1. Comparison of the Homogeneous and Heterogeneous options. Comparison of the results and cartographies obtained by MuscleJ2 after fiber morphology analysis on laminin-stained tibialis anterior sections after partial injury, with the Healthy option (left) and the Damaged option (right). Histograms at the bottom show the frequency of fibers with different cross-sectional areas. The results show that the number of included fibers is higher with the Damaged option than with the Healthy option, where numerous fibers are excluded from the analysis (black fibers). Fig. S2. Analysis of the diaphragm with MuscleJ2. A Cartography of the extracellular matrix (ECM) staining representing the diaphragm of the mouse rolled up on itself at the time of cutting. B Comparison of the results obtained by MuscleJ2 after ECM analysis on laminin-stained diaphragm sections with the Diaphragm option and the Limb option. The results show that the total surface area is smaller with the Diaphragm section due to the removal of the fiberless parts (*), which is not the case with the Limb option. Fig. S3. Comparison of the Data Acquisition panel between the macro and the plugin MuscleJ2. Screenshots of the dialog boxes in the initial macro (A) and the plugin (B) showing changes in the Data acquisition section. Fig. S4. Peri-myonuclei detection with MuscleJ2. A Skeletal muscle section from injured mouse (21 days post-injury) stained with DAPI, PCM1 and laminin antibodies (SB=500 µm) and representative cartography of perimyonuclei quantification results obtained with MuscleJ2. Only double PCM1/DAPI-positive cells in the ROIMB are quantified and represented in the cartography. B The gray table shows the results obtained from the "GlobalResults" file, and C The green table shows a subset of the results obtained from the "PeriMyoNucleiDetails" file. Fig. S5. Fiber typing with MuscleJ2. A Skeletal muscle section stained with DAPI, myosin heavy chain IIX, IIA, I and laminin antibodies (SB=600 µm). B Representative cartographies (original image, fiber morphology and fiber typing) of the results obtained with MuscleJ2 (SB=300 µm). C Global file results and fiber detail results. All areas are given in µm2. Fig. S6. Global information associated with a MuscleJ2 batch run. Screenshots of the BATCH_LOG text file corresponding to the meta data and the analysis performed during the batch run as well as channel attributions to keep a printout of options and global information. Sup. Table 1. Main features of tools and software available to perform a fully or semiautomatic analysis on skeletal muscle immunofluorescence images. List of abbreviations used: AI: artificial intelligence; DPI: days post injury; EBD: Evans blue dye; IF: immunofluorescence; IHC: immunohistochemistry; MYH: myosin heavy chain (gene); NCAM: neural cell adhesion molecule; PFA: paraformaldehyde; ref: reference. Sup. Table 2. List of antibodies and specific protocols used.