Dataset Information

Building a three-dimensional model of early-stage zebrafish embryo brain.

ABSTRACT: We introduce a computational approach to build three-dimensional (3D) surface mesh models of the early-stage zebrafish brain primordia from time-series microscopy images. The complexity of the early-stage brain primordia and lack of recognizable landmarks pose a distinct challenge for feature segmentation and 3D modeling. Additional difficulty arises because of noise and variations in pixel intensity. We overcome these by using a hierarchical approach in which simple geometric elements, such as "beads" and "bonds," are assigned to represent local features and their connectivity is used to smoothen the surface while retaining high-curvature regions. We apply our method to build models of two zebrafish embryo phenotypes at discrete time points between 19 and 28 h post-fertilization and collect measurements to quantify development. Our approach is fast and applicable to building models of other biological systems, as demonstrated by models from magnetic resonance images of the human fetal brain. The source code, input scripts, sample image files, and generated outputs are publicly available on GitHub.

SUBMITTER: Chang-Gonzalez AC

PROVIDER: S-EPMC8535780 | biostudies-literature | 2021 Sep

REPOSITORIES: biostudies-literature

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Building a three-dimensional model of early-stage zebrafish embryo brain.

Chang-Gonzalez Ana C AC Gibbs Holly C HC Lekven Arne C AC Yeh Alvin T AT Hwang Wonmuk W

Biophysical reports 20210719 1

We introduce a computational approach to build three-dimensional (3D) surface mesh models of the early-stage zebrafish brain primordia from time-series microscopy images. The complexity of the early-stage brain primordia and lack of recognizable landmarks pose a distinct challenge for feature segmentation and 3D modeling. Additional difficulty arises because of noise and variations in pixel intensity. We overcome these by using a hierarchical approach in which simple geometric elements, such as ...[more]

PMID: 34693392

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Project description:BackgroundConsidering the complexity of vascular or bronchial variations and the difficulty of nodule localization during segmental resection, the three-dimensional (3D) reconstruction and printing model can provide a guarantee for safe operation and, to some extent, can simplify the surgical procedure. We conducted this study to estimate the avail of 3D reconstruction and personalized model in anatomical partial-lobectomy (APL).MethodsWe prospectively collected and retrospectively reviewed the data of 298 cases who underwent APL in our institute from April 2017 to May 2019. The patients were divided into "3D-reconstruction" group (131 patients), "3D model" group (31 patients) and "non-3D" group (136 patients). We adopted the ANOVA analysis and Chi-square test to compare the perioperative data between the three groups. Subjective satisfaction questionnaires for surgeons were provided to evaluate the value of personalized 3D printed model.ResultsThe proportion of complex segmentectomy in 3D model group (87.1%) was significantly higher than that in the 3D-reconstruction group (60.3%) and non-3D group (55.9%) (P=0.006), and the average operation time of complex segmentectomy in 3D model group (99.56 minutes) was significantly shorter than that of the other group (all P<0.05). The average intraoperative blood loss in the 3D model group (12.9 mL) was significantly lower than that in the 3D reconstruction group (20.9 mL) (P=0.001) and non-3D group (18.2 mL) (P=0.022). For simple segmentectomy, the operation time, postoperative drainage, and postoperative hospital stay were similar among the three groups. The questionnaire survey showed that most surgeons were satisfied with the clinical effectiveness of the personalized 3D printed model.Conclusions3D printing technology can improve understanding of the anatomy, decrease the operation time, and reduce the potential risk of thoracoscopic anatomical partial lobectomy in stage I lung cancer. A pre-operative rating scale was designed to standardize the application of this technology.

Dataset Information

Building a three-dimensional model of early-stage zebrafish embryo brain.

Publications

Building a three-dimensional model of early-stage zebrafish embryo brain.

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