Journal: STAR Protocols

Article Title: Protocol to study synapse density or volume—SynDOVE—in brain using confocal microscopy and Imaris three-dimensional surface rendering software

doi: 10.1016/j.xpro.2026.104465

Figure Lengend Snippet: Conversion of ND2 files to IMS files Double-click image to automatically convert files to.ims format for Imaris. ND2 files will have the white 3D box and right-pointing arrow icons in the lower left corner. IMS files will have the 3D box icon in the lower left corner.

Article Snippet: • Below is a table ( ) that summarizes the recommended minimum image acquisition parameters for puncta detection and surface segmentation during 3D surface rendering in Imaris.

Techniques:

Journal: Science Advances

Article Title: A cross-tissue physicochemical causal chain underlying vertebrate mandibular morphogenesis

doi: 10.1126/sciadv.aec7997

Figure Lengend Snippet: ( A ) Temporal changes in head region organ and tissue morphologies, represented as polygons reconstructed from microscopy images, at 18, 24, and 36 hpf. BE and OE are shown as red open surfaces. The OE forms by invagination of the BE and comprises dorsal and ventral layers. The PA1 is absent at 18 hpf but becomes evident by 24 hpf; its ventral portion (presumptive Meckel’s region) lies within the ventral compartment formed by the OE. An optical sagittal section at 36 hpf is shown on the right. Nuclei were labeled by tdTomato–NLS mRNA injection. The OE (red) is sandwiched between dorsal and ventral PA1 mesenchyme (yellow). ( B ) Temporal changes in the vOE (red) and mandibular mesenchyme morphologies, visualized as polygons from microscopy images, at 36, 42, and 48 hpf. ( C ) Dorsal view of vOE cell trajectories from 36 to 48 hpf, mirrored across the midline. ( D ) Quantification of local tissue deformation within the vOE (dorsal view). The right half was divided into four subregions. Although vOE cells move in three dimensions, each subregion remains approximately planar during the analyzed time window. Deformations were therefore approximated as 2D linear transformations embedded in 3D space and mapped back onto the predeformation configuration at 36 hpf. The results are visualized as deviations from a circle (inward: shrinkage; outward: elongation). ( E ) Magnitude (top) and orientation (bottom) of deformation anisotropy within the vOE ( N = 3 embryos). Eigenvalues of the deformation tensor in the posterior half were closer to 1, indicating weaker in-plane deformation than in the anterior half. Polygons were mirrored across the midplane in (A) and (B).

Article Snippet: To visualize the spatial pattern of shha mRNA localization within internal embryonic tissues, we generated 3D surface masks in Imaris and extracted fluorescence within a subvolume that encompassed the ventral diencephalon, the mandibular mesenchyme, the OE, and the pharyngeal endoderm at 28 and 32 hpf.

Techniques: Microscopy, Labeling, Injection