Journal: bioRxiv

Article Title: Protein-lipid interactions drive presynaptic assembly upstream of cell adhesion molecules

doi: 10.1101/2023.11.17.567618

Figure Lengend Snippet: Supp 1A. Representative images of ROIs identified for DA9 neuron-specific CLA-1::GFP puncta in CTRL and nrx-1(-) strains. In each genotype, the top image is a representative linescan of CLA-1::GFP at presynapses, and the bottom image contains the ROIs (outlined in green) that were identified by our MATLAB script. The same thresholding and restriction parameters were applied to all images containing this marker. Scale, 5 μm. Supp 1B. Representative images of ROIs identified for an endogenous NRX-1::Skylan marker in a CTRL and syd-1(-) strain. The top image is a representative linescan of NRX-1::Skylan at synapses in the dorsal nerve cord, and the bottom image contains ROIs (outlined in green). The same thresholding and restriction parameters were applied to all images of the NRX-1::Skylan marker. Scale, 2.5 μm.

Article Snippet: Fluorescent puncta in the 32-bit linescan tifs were detected and segmented using a custom ROI-based MATLAB application (Image Processing Toolbox Release 2022a, The MathWorks, Inc.) that uses local means thresholding and ROI watershed segmentation followed by parametric restriction to remove noise pixels.

Techniques: Marker

Journal: Frontiers in Molecular Neuroscience

Article Title: Astrocytes and Microglia Exhibit Cell-Specific Ca 2+ Signaling Dynamics in the Murine Spinal Cord

doi: 10.3389/fnmol.2022.840948

Figure Lengend Snippet: Activity-based Ca 2+ signaling analysis for astroglia and microglia from acute preparations. (A–D) Representative Ca 2+ signaling analysis for astroglia [ (A) white matter ( wm ); (C) gray matter ( gm )] and microglia [ (B) wm ; (D) gm ] in acute slice preparations using the custom-made MATLAB-based software MSparkles. Maximum-intensity projection of the GCaMP3 signal for representative Fields of View [FOV; scale bar, 20 μm; (i)] over the entire recording time (up to 5 min), absolute intensity projection (ii) and selected regions of activity [ROAs; (iii)] automatically detected using variations in absolute intensity. Red arrows indicate the locations of selected ROAs. Representative time frames from the selected recordings [scale bar, 20 μm; (iv)] with red arrows indicating location of the selected ROAs if active in the displayed time frame. Normalized relative fluorescence intensity traces over time (ΔF/F 0 ) for the selected ROAs (v) with trace colors matching colors of the selected ROAs. Oblique sections indicate time points chosen for display. Automatically detected signals were pinpointed and color coded based on signal strength (μ + σ ≤ ΔF/F 0 ≤ μ + 2σ, blue; μ + 2σ < ΔF/F 0 ≤ μ + 3σ, green; ΔF/F 0 > μ + 3σ, red) calculated on the mean value (μ) and the corresponding standard deviation (σ) over all ROAs.

Article Snippet: To compare glial Ca 2+ dynamics, we took advantage of a custom-made MATLAB-based analysis software (MSparkles) that identifies fluorescence changes in an unbiased and morphology independent manner and determines signal peak as well as region of activity (ROA) associated parameters.

Techniques: Activity Assay, Software, Fluorescence, Standard Deviation

Journal: Frontiers in Molecular Neuroscience

Article Title: Astrocytes and Microglia Exhibit Cell-Specific Ca 2+ Signaling Dynamics in the Murine Spinal Cord

doi: 10.3389/fnmol.2022.840948

Figure Lengend Snippet: Activity-based in vivo Ca 2+ signaling analysis for astro- and microglia after chronic window implantation. (A–F) Representative Ca 2+ signaling analysis for (A,C,E) astroglia and (B,D,F) microglia monitored in vivo [ (A,B) day one ( d1 ); (C,D) day two ( d2 ); (E,F) day 7 ( d7 )] using the custom-made MATLAB-based software MSparkles. Maximum-intensity projection of GCaMP3 signals for representative FOV [scale bar, 20 μm; (i)] over the entire recording time (up to 5 min), absolute intensity projection (ii) and selected regions of activity [ROAs; (iii)] automatically detected using variations in the absolute intensity. Red arrows indicate location of the selected ROAs with representative time frames from the selected recordings [scale bar, 20 μm; (iv)]. Red arrows indicate the location of the selected ROAs if active in the displayed time frame. Normalized relative fluorescence intensity traces over time (ΔF/F 0 ) for the selected ROAs (v) with trace colors matching the colors of the selected ROAs and oblique sections indicating the time points chosen for display. Automatically detected signals were pinpointed and color coded based on signal strength (μ + σ ≤ ΔF/F 0 ≤ μ + 2σ, blue; μ + 2σ < ΔF/F 0 ≤ μ + 3σ, green; ΔF/F 0 > μ + 3σ, red) calculated on the mean value (μ) and the corresponding standard deviation (σ) over all ROAs.

Article Snippet: To compare glial Ca 2+ dynamics, we took advantage of a custom-made MATLAB-based analysis software (MSparkles) that identifies fluorescence changes in an unbiased and morphology independent manner and determines signal peak as well as region of activity (ROA) associated parameters.

Techniques: Activity Assay, In Vivo, Software, Fluorescence, Standard Deviation