3d reconstruction software  (Autodesk Inc)

Journal: bioRxiv

Article Title: O-GlcNAc Transferase Regulates GABAergic Synapse Organization and Receptor Composition

doi: 10.1101/2025.11.21.689700

Figure Lengend Snippet: A . Representative 3D-rendered dendritic segment illustrating how vGAT and gephyrin puncta were categorized for analysis, including colocalized, non-colocalized, and overlapped populations. B. Representative images of cultured hippocampal neurons transfected at DIV7 with expressing GFP alone (Control) or co-expressing GFP with OGT (OGT overexpression). Neurons were analyzed by triple immunofluorescence labeling for GFP (yellow), gephyrin (lilac), and vGAT (green). Scale bar, 5 μm (applies to all images). C. Quantification graphs of the effects of OGT overexpression in neurons on intensity, and size of gephyrin or vGAT puncta (Total, non-colocalization). D. Quantification of inhibitory synapse number (gephyrin and vGAT puncta) showing no significant changes following OGT deletion. E. Quantification of overlapped volume gephyrin and vGAT puncta, showing a significant increase in OGT overexpression neurons. Data are presented as S.E.M (*P < 0.05, **P < 0.01, ***P < 0.001; unpaired Student’s t test).

Article Snippet: Upon overexpressing OGT in sparse neurons, inhibitory synapses terminating on the overexpressed neuron were identified using 3D Imaris reconstruction software by measuring vGAT and gephyrin puncta intensity, size and number.

Techniques: Cell Culture, Transfection, Expressing, Control, Over Expression, Immunofluorescence, Labeling

Journal: bioRxiv

Article Title: O-GlcNAc Transferase Regulates GABAergic Synapse Organization and Receptor Composition

doi: 10.1101/2025.11.21.689700

Figure Lengend Snippet: A. Representative images of cultured hippocampal neurons transfected at DIV7 with GFP alone (Control) or GFP + Cre (OGT-KO). Neurons were analyzed by triple immunofluorescence labeling for GFP (yellow), α-GABA A γ2 (magenta), and vGAT (green). Shown are single-plane and 3D-rendered views of γ2 and vGAT puncta along dendritic segments, with merged images illustrating their spatial relationship. Scale bar, 5 μm (applies to all images). B . Quantification of γ2 and vGAT puncta number per 10 μm dendrite in control and OGT-KO neurons, shown for total and non-colocalized populations. No significant differences were observed . C. Quantification of γ2 puncta intensity and volume (total and non-colocalized with vGAT) showed that OGT-KO neurons exhibited significant increases in γ2 intensity compared with controls. D. Quantification of overlapped γ2–vGAT puncta volume, showing significantly increased overlap in OGT-KO neurons. Data are presented as S.E.M. *P < 0.05, **P < 0.01, ***P < 0.001; unpaired Student’s t test.

Article Snippet: Upon overexpressing OGT in sparse neurons, inhibitory synapses terminating on the overexpressed neuron were identified using 3D Imaris reconstruction software by measuring vGAT and gephyrin puncta intensity, size and number.

Techniques: Cell Culture, Transfection, Control, Immunofluorescence, Labeling

Journal: NPJ Digital Medicine

Article Title: Timelapse-based 3D reconstruction of blastocysts reveals 3D morphologies of human blastocysts

doi: 10.1038/s41746-025-02028-9

Figure Lengend Snippet: The left panel shows the distributions of each parameter (y-axis: number of blastocysts; x-axis: units of the parameter). The middle panel lists the parameter numbers, names, and definitions. a–c On the right illustrate the definitions of selected 3D morphological parameters. a ICM minor-to-major axis ratio, indicating how elongated the ICM shape is. b Spatial distance between the ICM and TE: R denotes blastocyst radius; d is the distance from the ICM centroid to the blastocyst centroid, reflecting ICM displacement. c Corresponding to parameters 19 and 20, the blastocyst is divided into eight equal quadrants (Q1–Q8) around its centroid. The ICM quadrant (Q ICM ) is defined as the quadrant containing the ICM centroid. These two parameters describe the spatial relationship between the ICM location and the spatial density distribution of TE cells. TE, Trophectoderm; ICM, Inner Cell Mass.

Article Snippet: Figure shows the Imaris software 3D reconstruction and verification results of blastocyst fluorescence staining.

Techniques:

Journal: NPJ Digital Medicine

Article Title: Timelapse-based 3D reconstruction of blastocysts reveals 3D morphologies of human blastocysts

doi: 10.1038/s41746-025-02028-9

Figure Lengend Snippet: a Comparison of 3D reconstructions obtained from fluorescence staining and from TL imaging, showing the morphology of the whole blastocyst, the ICM, and the TE. b Relative error between fluorescence-based and TL-based reconstructions. ICM, Inner Cell Mass; TE, Trophectoderm; TL, Time-Lapse.

Article Snippet: Figure shows the Imaris software 3D reconstruction and verification results of blastocyst fluorescence staining.

Techniques: Comparison, Fluorescence, Staining, Imaging

Journal: NPJ Digital Medicine

Article Title: Timelapse-based 3D reconstruction of blastocysts reveals 3D morphologies of human blastocysts

doi: 10.1038/s41746-025-02028-9

Figure Lengend Snippet: a Bubble plots showing the associations between individual 3D morphological parameters and two key clinical outcomes—clinical pregnancy rate (solid circles) and live birth rate (open circles)—in the overall dataset and in specific subgroups. Bubble size indicates the number of blastocysts, and P values from Wilcoxon rank sum tests are shown within each plot. b Pie chart illustrating the distribution of blastocyst grades in the study cohort. c Bar plots showing the P values from Wilcoxon rank sum tests for the associations between each 3D morphological parameter and newborn gender. ICM, Inner Cell Mass; TE, Trophectoderm.

Article Snippet: Figure shows the Imaris software 3D reconstruction and verification results of blastocyst fluorescence staining.

Techniques:

Journal: NPJ Digital Medicine

Article Title: Timelapse-based 3D reconstruction of blastocysts reveals 3D morphologies of human blastocysts

doi: 10.1038/s41746-025-02028-9

Figure Lengend Snippet: a Focal-plane interpolation approach. b Schematic of spherical approximation for multi-focal plane images. c Spatial contour segmentation of TE. d Auxiliary circular markings on focal planes. e Process for fitting the geometric structure to the TE and ICM. f The focal depth estimation process. g Obtaining peak focus positions along the z-axis (quoted from Wang et al.) . h Comparison of ICM boundaries in different focal planes for manual labeling and model predictions. i Schematic of hemispherical texture projection (quoted from Jiang et al.) j Textured map of the blastocyst’s external surface. k Texture-mapped 3D geometric model. l Various geometric shapes clarify the concept of the shape factor (quoted from Cao et al.) . m The improvement of cell edge sharpness and overall contrast by RLTV and AHE. n Performance of ICM and TE segmentation models in training and validation datasets. o Performance of the ICM segmentation model in the test dataset. p Performance of the TE segmentation model in the test dataset. AHE, Adaptive Histogram Equalization; IoU, Intersection over Union; RLTV, Richardson-Lucy with total Variation; TL, Time-Lapse.

Article Snippet: Figure shows the Imaris software 3D reconstruction and verification results of blastocyst fluorescence staining.

Techniques: Comparison, Labeling, Biomarker Discovery

Journal: NPJ Digital Medicine

Article Title: Timelapse-based 3D reconstruction of blastocysts reveals 3D morphologies of human blastocysts

doi: 10.1038/s41746-025-02028-9

Figure Lengend Snippet: The study workflow covers data acquisition, focal-plane image generation, ICM and TE segmentation, 3D reconstruction, validation of reconstructed models, and outcome analysis. FET, Frozen Embryo Transfer; 3D, Three-Dimensional; TE, Trophectoderm; ICM, Inner Cell Mass.

Article Snippet: Figure shows the Imaris software 3D reconstruction and verification results of blastocyst fluorescence staining.

Techniques: Biomarker Discovery

Journal: NPJ Digital Medicine

Article Title: Timelapse-based 3D reconstruction of blastocysts reveals 3D morphologies of human blastocysts

doi: 10.1038/s41746-025-02028-9

Figure Lengend Snippet: The 3D reconstruction workflow consists of geometric structure reconstruction (shown in purple) and texture feature reconstruction (shown in blue). ICM, Inner Cell Mass; TE, Trophectoderm; TL, Time-Lapse.

Article Snippet: Figure shows the Imaris software 3D reconstruction and verification results of blastocyst fluorescence staining.

Techniques:

Journal: Advanced Science

Article Title: Uric Acid Functions as an Endogenous Modulator of Microglial Function and Amyloid Clearance in Alzheimer's Disease

doi: 10.1002/advs.202510270

Figure Lengend Snippet: UA treatment enhances microglial phagocytosis of Aβ. A) Representative Imaris‐based 3D reconstruction of amyloid plaques (MX04, blue; 6E10, red) and microglia (Iba1, green). Scale bar, 10 µm; 5 µm in zoom‐in view. B) Quantification of the number of plaque‐associated microglia (n = 8 mice per group, 43 plaques for 5×FAD+Veh and 44 plaques for 5×FAD+UA). C) Quantification of the MX04 internalization by microglia. n = 53–55 plaques from 10 volumetric images of 8 mice per group. D) Flow cytometric quantification of microglial and macrophage populations in 5×FAD+Veh and 5×FAD+UA mice (n = 8 mice per group). E) Representative flow cytometry plots and F) quantification of MX04 + CD11b + CD45 int hippocampal microglia from WT+Veh, 5×FAD+Veh, and 5×FAD+UA mice (n = 8 mice per group). G) Representative confocal z‐stack images and H) flow cytometry histograms of primary microglia exposed to FAM‐oAβ 1‐42 (1 µ m , 3 h) following treatment with vehicle or UA (100 µ m , 12 h). I) Quantification of mean fluorescence intensity (MFI) from (H) (n = 3 independent experiments). J) Flow cytometry analysis of endocytic capacity using FITC‐conjugated dextran (1 µg mL −1 , 3 h; n = 3 independent experiments). Data are presented as mean ± SEM. P values were determined by two‐tailed unpaired Student's t ‐test in (B, C, D macrophage, F, I, and J), and two‐tailed Mann–Whitney test in (D microglia). ns, not significant; * P < 0.05; ** P < 0.01; **** P < 0.0001.

Article Snippet: 3D reconstruction utilized Imaris software (v.10.0.0; Bitplane) for surface rendering of microglia and MX04‐positive dense‐core plaques, distance measurement between Iba1 surface centroids and the nearest plaque edge (MATLAB), and quantification of plaque‐associated microglia (≤15 μm from plaque edge).

Techniques: Flow Cytometry, Fluorescence, Two Tailed Test, MANN-WHITNEY