semi-automated matlab script  (MathWorks Inc)

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

Journal: Investigative Ophthalmology & Visual Science

Article Title: Semi-Automated Analysis of Dome-Shaped Macula in Preterm and Full-Term Infants Using Handheld Swept-Source Optical Coherence Tomography

doi: 10.1167/iovs.65.12.35

Figure Lengend Snippet: Example of dome-shaped macula measurements using the semi-automated MATLAB program. The grader selected a high-quality B scan including the foveal center for analysis. The dome width was measured at the base from inflection point to inflection point of the retinal pigment epithelium, selected by the grader. The dome height was measured from the base to the peak of the retinal pigment epithelium, whose location was selected by the grader.

Article Snippet: A novel semi-automated program in MATLAB (MathWorks, Inc., Natick, MA, USA) measured the dome diameter by tangentially connecting the two points of the retinal pigment epithelium at the base of the dome, selected by the grader at the inflection point on each side (see ).

Techniques: