Fraunhofer Portugal AICOS EDoF Dataset
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The Fraunhofer Portugal AICOS EDoF Dataset was produced within the TAMI project and is composed of images of microscopic fields of view (FOV) of Liquid-based Cervical Cytology (LBC) samples. A total of 15 LBC samples were supplied by the Pathology Services from Hospital Fernando Fonseca and the Portuguese Oncology Institute of Porto. For each LBC sample, a set of images were obtained using a version of µSmartScope [1,2] prototype adapted to the cervical cytology use case [3,4]. µSmartScope is a portable 3D-printed prototype based on a smartphone developed by Fraunhofer AICOS that allows the fully automatic acquisition of microscopic images. The acquisition is done using the automated focus approach described in [1], where for each FOV, all images in the precise phase of the approach are stored as well as an indication of the image with the best focus metric (standard deviation of the Tenenbaum gradient [5]). The dataset is divided into two partitions: the first partition contains the raw data with 5 images per stack without any pre-processing; the second partition contains the pre-processed data according to the best workflow proposed in [6], and also the respective EDoF generated using Complex Wavelets method for the fusion of the microscopy Images. The images from the second partition were pre-processed using chromatic, static, and elastic alignment; they can be used to fully replicate the work in [6]. The size of every image present in this database is 960x720 pixels. For this work, 144 EDoFs images generated with 5 aligned images per stack are used (where the central image is the one with the best focus metric (C). Figure 1 shows an example of a stack and the respective EDoF. If you find this dataset useful for your research, please cite as: T. Albuquerque, L. Rosado, R. Cruz, M. J. M. Vasconcelos, T. Oliveira J. S. Cardoso, Rethinking Low-Cost Microscopy Workflow: Image Enhancement using Deep Based Extended Depth of Field Methods, In Intelligent Systems with Applications (Elsevier), 2023. https://doi.org/10.1016/j.iswa.2022.200170.
弗劳恩霍夫葡萄牙AICOS扩展景深（Extended Depth of Field, EDoF）数据集由TAMI项目研发生成，其数据源自液基宫颈细胞学（Liquid-based Cervical Cytology, LBC）样本的显微视场（Field of View, FOV）图像。葡萄牙费尔南多·丰塞卡医院病理科与葡萄牙波尔图肿瘤研究所共提供了15份LBC样本。针对每份LBC样本，研究团队采用适配宫颈细胞学应用场景的改良版µSmartScope原型[1,2,3,4]采集了一系列图像。µSmartScope是由弗劳恩霍夫AICOS开发的基于智能手机的便携式3D打印原型设备，可实现显微图像的全自动采集。其采集流程采用文献[1]中所述的自动对焦方案：针对每个视场，采集对焦过程中各精确相位下的全部图像，并存储对焦效果最优的图像的标识——该最优图像以特南鲍姆梯度的标准差[5]作为对焦评价指标。本数据集分为两个分区：第一分区为原始数据，每个图像栈包含5张未经过任何预处理的图像；第二分区为经过预处理的数据，其预处理流程采用文献[6]中提出的最优工作流，同时还包含基于复小波（Complex Wavelets）图像融合方法生成的对应EDoF图像。第二分区的图像经过色度对齐、静态对齐与弹性对齐预处理，可完全复现文献[6]中的研究工作。本数据库内所有图像的分辨率均为960×720像素。本次研究使用了由每个图像栈的5张对齐图像生成的144张EDoF图像，其中每栈的中心图像即为对焦效果最优的图像（记为C）。图1展示了一个图像栈及其对应的EDoF图像示例。若您的研究中使用本数据集，请引用如下文献：T. Albuquerque, L. Rosado, R. Cruz, M. J. M. Vasconcelos, T. Oliveira J. S. Cardoso, 《Rethinking Low-Cost Microscopy Workflow: Image Enhancement using Deep-Based Extended Depth of Field Methods》，发表于《Intelligent Systems with Applications》（爱思唯尔Elsevier），2023年，https://doi.org/10.1016/j.iswa.2022.200170。
