Quantitative imaging of epithelial tissues prompts for bioimage analysis tools that are widely applicable and accurate. In the case of imaging 3D tissues, a common preprocessing step consists in projecting the acquired 3D volume on a 2D plane mapping the tissue surface. Indeed, while segmenting the tissue cells is amenable on 2D projections, it is still very difficult and cumbersome in 3D. However, for many specimen and models used in Developmental and Cell Biology, the complex content of the image volume surrounding the epithelium in a tissue often reduces the visibility of the biological object in the projection, compromising its subsequent analysis. In addition, the projection may distort the geometry of the tissue and can lead to strong artifacts in the morphology measurement. Here we introduce a user-friendly toolbox built to robustly project epithelia on their 2D surface from 3D volumes, and to produce accurate morphology measurement corrected for the projection distortion, even for very curved tissues. Our toolbox is built upon two components. LocalZProjector is a user-friendly and configurable Fiji plugin that generates 2D projections and height-maps from potentially large 3D stacks (larger than 40 GB per time-point) by only incorporating signal of the planes with local highest variance/mean intensity, despite a possibly complex image content. DeProj is a MATLAB tool that generates correct morphology measurements by combining the height-map output (such as the one offered by LocalZProjector) and the results of a cell segmentation on the 2D projection, hence effectively deprojecting the 2D segmentation in 3D. In this paper we demonstrate their effectiveness over a wide range of different biological samples. We then compare its performance and accuracy against similar existing tools. We find that LocalZProjector performs well even in situations where the volume to project also contains unwanted signal in other layers . We show that it can process large images without a pre-processing step. We study the impact of geometrical distortions on morphological measurements induced by the projection. We measured very large distortions which are then corrected by DeProj, providing accurate outputs.

中文翻译：

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LocalZProjector和DeProj：用于大型2D显微图像的局部2D投影和精确形态计量学的工具箱。

上皮组织的定量成像提示了广泛适用和准确的生物图像分析工具。在对3D组织成像的情况下，常见的预处理步骤包括将获取的3D体积投影到映射组织表面的2D平面上。确实，尽管在2D投影上可以对组织细胞进行分割，但在3D中仍然非常困难且麻烦。然而，对于发育和细胞生物学中使用的许多标本和模型，组织中上皮周围图像体积的复杂含量通常会降低投影中生物对象的可见性，从而损害其后续分析。另外，投影可能会使组织的几何形状变形，并可能导致形态测量中出现强烈的伪影。在这里，我们介绍了一种用户友好的工具箱，该工具箱可将3d体积的2D表面牢固地投射到2D表面上，并产生针对投影畸变校正的准确形态学测量结果，即使是非常弯曲的组织也是如此。我们的工具箱基于两个组件。LocalZProjector是一个用户友好且可配置的斐济插件，它通过仅合并具有局部最大方差/平均强度的平面信号，从潜在的大型3D堆栈（每个时间点大于40 GB）生成2D投影和高度图。可能是复杂的图像内容。DeProj是一种MATLAB工具，可通过结合高度图输出（例如LocalZProjector提供的高度图）和2D投影上的细胞分割结果来生成正确的形态学测量值，从而有效地将3D分割投影到3D中。在本文中，我们证明了它们在各种不同生物样品中的有效性。然后，我们将其性能和准确性与类似的现有工具进行比较。我们发现，即使在要投影的体积在其他层中也包含有害信号的情况下，LocalZProjector的性能也很好。我们证明了它可以处理大型图像而无需预处理步骤。我们研究了几何变形对投影引起的形态测量的影响。我们测量了非常大的失真，然后由DeProj对其进行校正，以提供准确的输出。我们发现，即使在要投影的体积在其他层中也包含有害信号的情况下，LocalZProjector的性能也很好。我们证明了它可以处理大型图像而无需预处理步骤。我们研究了几何变形对投影引起的形态测量的影响。我们测量了非常大的失真，然后由DeProj对其进行校正，以提供准确的输出。我们发现，即使在要投影的体积在其他层中也包含有害信号的情况下，LocalZProjector的性能也很好。我们证明了它可以处理大型图像而无需预处理步骤。我们研究了几何变形对投影引起的形态测量的影响。我们测量了非常大的失真，然后由DeProj对其进行校正，以提供准确的输出。