Origami: Single-cell 3D shape dynamics oriented along the apico-basal axis of folding epithelia from fluorescence microscopy data.
Origami: Single-cell 3D shape dynamics oriented along the apico-basal axis of folding epithelia from fluorescence microscopy data.
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DOI：
10.1371/journal.pcbi.1009063
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发表时间：
2021-11
影响因子：
4.3
通讯作者：
Frangi AF
中科院分区：
文献类型：
--
作者：
Mendonca T;Jones AA;Pozo JM;Baxendale S;Whitfield TT;Frangi AF
形态发生的一个共同特征是在细胞水平上的细胞形状变化的辅助下，由二维上皮片的折叠形成三维结构。细胞形状的变化必须在上皮片内细胞极化的生物力学过程的背景下进行研究。在具有高度曲面的上皮细胞中，在Silico中很难自动找到沿着生物轴的单细胞排列。我们提出了一个基于MatLab的图像分析流水线，用于计算沿上皮心尖-基底轴方向变化的细胞形状特征。我们的自动化方法准确地计算出指示合成上皮和斑马鱼胚胎荧光图像中相反曲率区域的顶基轴的方向向量。作为概念的证明，我们在斑马鱼发育的内耳中识别出不同的细胞形状特征，其中的上皮细胞以相反的方向变形，形成不同的结构。折纸的设计是用户友好的，通常适用于弯曲上皮的荧光图像。在胚胎发育期间，二维上皮片弯曲并折叠成复杂的三维结构-就像折纸艺术形式中的纸。驱动上皮折叠的遗传和生物力学过程可以在上皮中极化，导致单细胞水平上的不对称形状变化。这种上皮形成的缺陷与许多发育异常和疾病有关。因此，重要的是不仅要在单细胞水平上量化形状变化，而且在研究形态发生过程时，也要沿着上皮极性轴定位这些不对称的变化。折纸是一个基于MatLab的软件，它被开发来自动从折叠上皮的荧光显微镜图像中提取沿着上皮尖基轴的单细胞不对称形状特征。折纸提供了一种解决方案，计算沿上皮心尖-基轴的方向向量，然后提取每个分割细胞的方向变化的形状特征。它一般适用于上皮结构，无论折叠的复杂程度或方向如何，对成像条件都是健壮的。作为概念的证明，在斑马鱼内耳的不同发育时间点，折纸成功地在高度弯曲的结构中区分出不同的细胞形状特征。
A common feature of morphogenesis is the formation of three-dimensional structures from the folding of two-dimensional epithelial sheets, aided by cell shape changes at the cellular-level. Changes in cell shape must be studied in the context of cell-polarised biomechanical processes within the epithelial sheet. In epithelia with highly curved surfaces, finding single-cell alignment along a biological axis can be difficult to automate in silico. We present ‘Origami’, a MATLAB-based image analysis pipeline to compute direction-variant cell shape features along the epithelial apico-basal axis. Our automated method accurately computed direction vectors denoting the apico-basal axis in regions with opposing curvature in synthetic epithelia and fluorescence images of zebrafish embryos. As proof of concept, we identified different cell shape signatures in the developing zebrafish inner ear, where the epithelium deforms in opposite orientations to form different structures. Origami is designed to be user-friendly and is generally applicable to fluorescence images of curved epithelia. During embryonic development, two-dimensional epithelial sheets bend and fold into complex three-dimensional structures–like paper in the origami art form. The genetic and biomechanical processes driving epithelial folding can be polarised in the epithelium, leading to asymmetric shape changes at the single cell level. Defects in such epithelial shaping have been linked to many developmental anomalies and diseases. It is, therefore, important not only to quantify shape change at the single cell level, but also to orientate these asymmetrical changes along an epithelial axis of polarity when studying morphogenetic processes. Origami is a MATLAB-based software that has been developed to automatically extract such single-cell asymmetrical shape features along the epithelial apico-basal axis from fluorescence microscopy images of folding epithelia. Origami provides a solution to computing directional vectors along the epithelial apico-basal axis followed by extracting direction-variant shape features of each segmented cell. It is generally applicable to epithelial structures regardless of complexity or direction of folding and is robust to imaging conditions. As proof of concept, Origami successfully differentiated between different cell shape signatures in highly curved structures at different developmental timepoints in the zebrafish inner ear.
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影响因子：
7.7
作者：
Barbier de Reuille P;Routier-Kierzkowska AL;Kierzkowski D;Bassel GW;Schüpbach T;Tauriello G;Bajpai N;Strauss S;Weber A;Kiss A;Burian A;Hofhuis H;Sapala A;Lipowczan M;Heimlicher MB;Robinson S;Bayer EM;Basler K;Koumoutsakos P;Roeder AH;Aegerter-Wilmsen T;Nakayama N;Tsiantis M;Hay A;Kwiatkowska D;Xenarios I;Kuhlemeier C;Smith RS
通讯作者：
Smith RS
影响因子：
9.8
作者：
McQuin C;Goodman A;Chernyshev V;Kamentsky L;Cimini BA;Karhohs KW;Doan M;Ding L;Rafelski SM;Thirstrup D;Wiegraebe W;Singh S;Becker T;Caicedo JC;Carpenter AE
通讯作者：
Carpenter AE
影响因子：
3.7
作者：
Ichikawa T;Nakazato K;Keller PJ;Kajiura-Kobayashi H;Stelzer EH;Mochizuki A;Nonaka S
通讯作者：
Nonaka S
影响因子：
11.8
作者：
Heller D;Hoppe A;Restrepo S;Gatti L;Tournier AL;Tapon N;Basler K;Mao Y
通讯作者：
Mao Y
DOI：
10.1242/dev.098061
发表时间：
2013-11
期刊：
Development (Cambridge, England)
影响因子：
--
作者：
Geng FS;Abbas L;Baxendale S;Holdsworth CJ;Swanson AG;Slanchev K;Hammerschmidt M;Topczewski J;Whitfield TT
通讯作者：
Whitfield TT