MIST: Accurate and Scalable Microscopy Image Stitching Tool with Stage Modeling and Error Minimization.
MIST: Accurate and Scalable Microscopy Image Stitching Tool with Stage Modeling and Error Minimization.
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DOI：
10.1038/s41598-017-04567-y
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发表时间：
2017-07-10
影响因子：
4.6
通讯作者：
Brady M
中科院分区：
文献类型：
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作者：
Chalfoun J;Majurski M;Blattner T;Bhadriraju K;Keyrouz W;Bajcsy P;Brady M
自动显微镜可以通过拼接重叠的图像块来成像比显微镜视场(FOV)更大的样品。它还可以在多种成像方式下对整个细胞培养进行延时研究。我们开发了MIST(显微图像拼接工具)，用于快速准确地拼接大型2D延时马赛克。MIST根据计算的两两平移估计机械工作台模型参数(致动器间隙和工作台重复性‘r’)，然后通过在(4r)2平方面积内优化平移来最大限度地减少缝合误差。MIST采用以性能为导向的实施方案，利用多核混合CPU/GPU计算资源，处理TB级的延时多通道马赛克的速度比现有工具快15到100倍。我们创建了15个参考数据集来量化MIST的拼接精度。数据集包括三种干细胞集落，以低密度播种，并以不同的重叠(10%至50%)进行成像。测量了1150个菌落的位置和大小，以量化拼接精度。Mist生成的拼接图像的平均质心距离误差小于FOV的2%。这些误差的来源包括机械不确定性、样本光漂白、分割和缝合不准确。Mist的拼接精度比三款开源工具都要高。Mist可以在isg.nist.gov的ImageJ中找到。
Automated microscopy can image specimens larger than the microscope’s field of view (FOV) by stitching overlapping image tiles. It also enables time-lapse studies of entire cell cultures in multiple imaging modalities. We created MIST (Microscopy Image Stitching Tool) for rapid and accurate stitching of large 2D time-lapse mosaics. MIST estimates the mechanical stage model parameters (actuator backlash, and stage repeatability ‘r’) from computed pairwise translations and then minimizes stitching errors by optimizing the translations within a (4r)2 square area. MIST has a performance-oriented implementation utilizing multicore hybrid CPU/GPU computing resources, which can process terabytes of time-lapse multi-channel mosaics 15 to 100 times faster than existing tools. We created 15 reference datasets to quantify MIST’s stitching accuracy. The datasets consist of three preparations of stem cell colonies seeded at low density and imaged with varying overlap (10 to 50%). The location and size of 1150 colonies are measured to quantify stitching accuracy. MIST generated stitched images with an average centroid distance error that is less than 2% of a FOV. The sources of these errors include mechanical uncertainties, specimen photobleaching, segmentation, and stitching inaccuracies. MIST produced higher stitching accuracy than three open-source tools. MIST is available in ImageJ at isg.nist.gov.