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matlab-based semi-automated rgc counting algorithm  (MathWorks Inc)


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    MathWorks Inc matlab-based semi-automated rgc counting algorithm
    a Diagram of experimental paradigm showing how eyes were either evaluated for synaptic pathology (left) via cross-sections or <t>retinal</t> <t>ganglion</t> <t>cell</t> <t>(RGC)</t> loss via flat mounts (right) on EAE d16 mice. b Representative image of flat-mounted retina with 12 regions selected for Brn3a + RGC quantification. Scale bar in full retina image = 500 μm, in high magnification counting fields scale bar = 20 μm. c Quantification of Brn3a + RGCs at peak EAE. N = 4 per experimental group. d Quantification of the integrated density of markers Syn1 (left) and PSD95 (right) in the inner plexiform layer of CFA vs GFAP-Cre animals at peak EAE. Signal intensity values are normalized to CFA control, with AU representing “arbitrary units”. N = 4 CFA, 10 GFAP-Cre − and 7 GFAP-Cre + mice. e Representative immunofluorescent staining of Syn1 (red) and PSD95 (green) in the inner and outer plexiform layers across GFAP-Cre experimental groups. Scale bar = 50 um. f Same as in e but evaluating synaptic markers in the inner plexiform layer of LysM-Cre + and LysM-Cre − mice. Values are normalized to the CFA only animals utilized in Fig. 5d. N = 4 CFA, 6 LysM-Cre − and 8 LysM-Cre + mice. g Representative immunofluorescent staining of Syn1 and PSD95 in LysM-Cre − vs LysM-Cre + mice. Scale bar = 50 um. All bar graphs presented as mean +/- SEM, with one-way ANOVAs adjusted for multiple comparisons. Source data are provided as a source data file. Figure 5a created in BioRender. Smith, M. (2025) https://BioRender.com/j21s335 .
    Matlab Based Semi Automated Rgc Counting Algorithm, supplied by MathWorks Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/semi-automated+matlab+algorithm/pmc11992029-349-2-1
    Average 90 stars, based on 1 article reviews
    matlab-based semi-automated rgc counting algorithm - by Bioz Stars, 2026-11
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    1) Product Images from "Myeloid lineage C3 induces reactive gliosis and neuronal stress during CNS inflammation"

    Article Title: Myeloid lineage C3 induces reactive gliosis and neuronal stress during CNS inflammation

    Journal: Nature Communications

    doi: 10.1038/s41467-025-58708-3

    a Diagram of experimental paradigm showing how eyes were either evaluated for synaptic pathology (left) via cross-sections or retinal ganglion cell (RGC) loss via flat mounts (right) on EAE d16 mice. b Representative image of flat-mounted retina with 12 regions selected for Brn3a + RGC quantification. Scale bar in full retina image = 500 μm, in high magnification counting fields scale bar = 20 μm. c Quantification of Brn3a + RGCs at peak EAE. N = 4 per experimental group. d Quantification of the integrated density of markers Syn1 (left) and PSD95 (right) in the inner plexiform layer of CFA vs GFAP-Cre animals at peak EAE. Signal intensity values are normalized to CFA control, with AU representing “arbitrary units”. N = 4 CFA, 10 GFAP-Cre − and 7 GFAP-Cre + mice. e Representative immunofluorescent staining of Syn1 (red) and PSD95 (green) in the inner and outer plexiform layers across GFAP-Cre experimental groups. Scale bar = 50 um. f Same as in e but evaluating synaptic markers in the inner plexiform layer of LysM-Cre + and LysM-Cre − mice. Values are normalized to the CFA only animals utilized in Fig. 5d. N = 4 CFA, 6 LysM-Cre − and 8 LysM-Cre + mice. g Representative immunofluorescent staining of Syn1 and PSD95 in LysM-Cre − vs LysM-Cre + mice. Scale bar = 50 um. All bar graphs presented as mean +/- SEM, with one-way ANOVAs adjusted for multiple comparisons. Source data are provided as a source data file. Figure 5a created in BioRender. Smith, M. (2025) https://BioRender.com/j21s335 .
    Figure Legend Snippet: a Diagram of experimental paradigm showing how eyes were either evaluated for synaptic pathology (left) via cross-sections or retinal ganglion cell (RGC) loss via flat mounts (right) on EAE d16 mice. b Representative image of flat-mounted retina with 12 regions selected for Brn3a + RGC quantification. Scale bar in full retina image = 500 μm, in high magnification counting fields scale bar = 20 μm. c Quantification of Brn3a + RGCs at peak EAE. N = 4 per experimental group. d Quantification of the integrated density of markers Syn1 (left) and PSD95 (right) in the inner plexiform layer of CFA vs GFAP-Cre animals at peak EAE. Signal intensity values are normalized to CFA control, with AU representing “arbitrary units”. N = 4 CFA, 10 GFAP-Cre − and 7 GFAP-Cre + mice. e Representative immunofluorescent staining of Syn1 (red) and PSD95 (green) in the inner and outer plexiform layers across GFAP-Cre experimental groups. Scale bar = 50 um. f Same as in e but evaluating synaptic markers in the inner plexiform layer of LysM-Cre + and LysM-Cre − mice. Values are normalized to the CFA only animals utilized in Fig. 5d. N = 4 CFA, 6 LysM-Cre − and 8 LysM-Cre + mice. g Representative immunofluorescent staining of Syn1 and PSD95 in LysM-Cre − vs LysM-Cre + mice. Scale bar = 50 um. All bar graphs presented as mean +/- SEM, with one-way ANOVAs adjusted for multiple comparisons. Source data are provided as a source data file. Figure 5a created in BioRender. Smith, M. (2025) https://BioRender.com/j21s335 .

    Techniques Used: Control, Staining

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    a Diagram of experimental paradigm showing how eyes were either evaluated for synaptic pathology (left) via cross-sections or <t>retinal</t> <t>ganglion</t> <t>cell</t> <t>(RGC)</t> loss via flat mounts (right) on EAE d16 mice. b Representative image of flat-mounted retina with 12 regions selected for Brn3a + RGC quantification. Scale bar in full retina image = 500 μm, in high magnification counting fields scale bar = 20 μm. c Quantification of Brn3a + RGCs at peak EAE. N = 4 per experimental group. d Quantification of the integrated density of markers Syn1 (left) and PSD95 (right) in the inner plexiform layer of CFA vs GFAP-Cre animals at peak EAE. Signal intensity values are normalized to CFA control, with AU representing “arbitrary units”. N = 4 CFA, 10 GFAP-Cre − and 7 GFAP-Cre + mice. e Representative immunofluorescent staining of Syn1 (red) and PSD95 (green) in the inner and outer plexiform layers across GFAP-Cre experimental groups. Scale bar = 50 um. f Same as in e but evaluating synaptic markers in the inner plexiform layer of LysM-Cre + and LysM-Cre − mice. Values are normalized to the CFA only animals utilized in Fig. 5d. N = 4 CFA, 6 LysM-Cre − and 8 LysM-Cre + mice. g Representative immunofluorescent staining of Syn1 and PSD95 in LysM-Cre − vs LysM-Cre + mice. Scale bar = 50 um. All bar graphs presented as mean +/- SEM, with one-way ANOVAs adjusted for multiple comparisons. Source data are provided as a source data file. Figure 5a created in BioRender. Smith, M. (2025) https://BioRender.com/j21s335 .
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    a Diagram of experimental paradigm showing how eyes were either evaluated for synaptic pathology (left) via cross-sections or <t>retinal</t> <t>ganglion</t> <t>cell</t> <t>(RGC)</t> loss via flat mounts (right) on EAE d16 mice. b Representative image of flat-mounted retina with 12 regions selected for Brn3a + RGC quantification. Scale bar in full retina image = 500 μm, in high magnification counting fields scale bar = 20 μm. c Quantification of Brn3a + RGCs at peak EAE. N = 4 per experimental group. d Quantification of the integrated density of markers Syn1 (left) and PSD95 (right) in the inner plexiform layer of CFA vs GFAP-Cre animals at peak EAE. Signal intensity values are normalized to CFA control, with AU representing “arbitrary units”. N = 4 CFA, 10 GFAP-Cre − and 7 GFAP-Cre + mice. e Representative immunofluorescent staining of Syn1 (red) and PSD95 (green) in the inner and outer plexiform layers across GFAP-Cre experimental groups. Scale bar = 50 um. f Same as in e but evaluating synaptic markers in the inner plexiform layer of LysM-Cre + and LysM-Cre − mice. Values are normalized to the CFA only animals utilized in Fig. 5d. N = 4 CFA, 6 LysM-Cre − and 8 LysM-Cre + mice. g Representative immunofluorescent staining of Syn1 and PSD95 in LysM-Cre − vs LysM-Cre + mice. Scale bar = 50 um. All bar graphs presented as mean +/- SEM, with one-way ANOVAs adjusted for multiple comparisons. Source data are provided as a source data file. Figure 5a created in BioRender. Smith, M. (2025) https://BioRender.com/j21s335 .
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    a Diagram of experimental paradigm showing how eyes were either evaluated for synaptic pathology (left) via cross-sections or <t>retinal</t> <t>ganglion</t> <t>cell</t> <t>(RGC)</t> loss via flat mounts (right) on EAE d16 mice. b Representative image of flat-mounted retina with 12 regions selected for Brn3a + RGC quantification. Scale bar in full retina image = 500 μm, in high magnification counting fields scale bar = 20 μm. c Quantification of Brn3a + RGCs at peak EAE. N = 4 per experimental group. d Quantification of the integrated density of markers Syn1 (left) and PSD95 (right) in the inner plexiform layer of CFA vs GFAP-Cre animals at peak EAE. Signal intensity values are normalized to CFA control, with AU representing “arbitrary units”. N = 4 CFA, 10 GFAP-Cre − and 7 GFAP-Cre + mice. e Representative immunofluorescent staining of Syn1 (red) and PSD95 (green) in the inner and outer plexiform layers across GFAP-Cre experimental groups. Scale bar = 50 um. f Same as in e but evaluating synaptic markers in the inner plexiform layer of LysM-Cre + and LysM-Cre − mice. Values are normalized to the CFA only animals utilized in Fig. 5d. N = 4 CFA, 6 LysM-Cre − and 8 LysM-Cre + mice. g Representative immunofluorescent staining of Syn1 and PSD95 in LysM-Cre − vs LysM-Cre + mice. Scale bar = 50 um. All bar graphs presented as mean +/- SEM, with one-way ANOVAs adjusted for multiple comparisons. Source data are provided as a source data file. Figure 5a created in BioRender. Smith, M. (2025) https://BioRender.com/j21s335 .
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    Image Search Results


    a Diagram of experimental paradigm showing how eyes were either evaluated for synaptic pathology (left) via cross-sections or retinal ganglion cell (RGC) loss via flat mounts (right) on EAE d16 mice. b Representative image of flat-mounted retina with 12 regions selected for Brn3a + RGC quantification. Scale bar in full retina image = 500 μm, in high magnification counting fields scale bar = 20 μm. c Quantification of Brn3a + RGCs at peak EAE. N = 4 per experimental group. d Quantification of the integrated density of markers Syn1 (left) and PSD95 (right) in the inner plexiform layer of CFA vs GFAP-Cre animals at peak EAE. Signal intensity values are normalized to CFA control, with AU representing “arbitrary units”. N = 4 CFA, 10 GFAP-Cre − and 7 GFAP-Cre + mice. e Representative immunofluorescent staining of Syn1 (red) and PSD95 (green) in the inner and outer plexiform layers across GFAP-Cre experimental groups. Scale bar = 50 um. f Same as in e but evaluating synaptic markers in the inner plexiform layer of LysM-Cre + and LysM-Cre − mice. Values are normalized to the CFA only animals utilized in Fig. 5d. N = 4 CFA, 6 LysM-Cre − and 8 LysM-Cre + mice. g Representative immunofluorescent staining of Syn1 and PSD95 in LysM-Cre − vs LysM-Cre + mice. Scale bar = 50 um. All bar graphs presented as mean +/- SEM, with one-way ANOVAs adjusted for multiple comparisons. Source data are provided as a source data file. Figure 5a created in BioRender. Smith, M. (2025) https://BioRender.com/j21s335 .

    Journal: Nature Communications

    Article Title: Myeloid lineage C3 induces reactive gliosis and neuronal stress during CNS inflammation

    doi: 10.1038/s41467-025-58708-3

    Figure Lengend Snippet: a Diagram of experimental paradigm showing how eyes were either evaluated for synaptic pathology (left) via cross-sections or retinal ganglion cell (RGC) loss via flat mounts (right) on EAE d16 mice. b Representative image of flat-mounted retina with 12 regions selected for Brn3a + RGC quantification. Scale bar in full retina image = 500 μm, in high magnification counting fields scale bar = 20 μm. c Quantification of Brn3a + RGCs at peak EAE. N = 4 per experimental group. d Quantification of the integrated density of markers Syn1 (left) and PSD95 (right) in the inner plexiform layer of CFA vs GFAP-Cre animals at peak EAE. Signal intensity values are normalized to CFA control, with AU representing “arbitrary units”. N = 4 CFA, 10 GFAP-Cre − and 7 GFAP-Cre + mice. e Representative immunofluorescent staining of Syn1 (red) and PSD95 (green) in the inner and outer plexiform layers across GFAP-Cre experimental groups. Scale bar = 50 um. f Same as in e but evaluating synaptic markers in the inner plexiform layer of LysM-Cre + and LysM-Cre − mice. Values are normalized to the CFA only animals utilized in Fig. 5d. N = 4 CFA, 6 LysM-Cre − and 8 LysM-Cre + mice. g Representative immunofluorescent staining of Syn1 and PSD95 in LysM-Cre − vs LysM-Cre + mice. Scale bar = 50 um. All bar graphs presented as mean +/- SEM, with one-way ANOVAs adjusted for multiple comparisons. Source data are provided as a source data file. Figure 5a created in BioRender. Smith, M. (2025) https://BioRender.com/j21s335 .

    Article Snippet: Our MATLAB-based semi-automated RGC counting algorithm was used to determine RGC number in each mouse .

    Techniques: Control, Staining