Springer Nature

A large-scale three-fold annotated microscopy image dataset of potato tubers for deep learning-based plant cell assessment

Posted on 2020-10-21 - 08:31
This dataset includes 9,811 natural (unstained) and 6,127 stained brightfield microscopy images with three fold annotation such as physical, morphological and tissue grading based on weight, different section area and tissue zone respectively. The tuber weight ranging from 80-100 gm, 40-50 gm, 15-25 gm have been considered as large (L), medium (M), and small (S) respectively. Furthermore, the images have been labelled with L, M, and S to specify their respective weights. Further, the samples associated with each label have been numbered from 1 to 5, such as L1 refers to the first sample of a large tuber. For morphological grading, the tubers have been divided into three parts namely Z1, Z2, and Z3 which specify the bud, middle, and stem areas respectively. In tissue grading, the images have been captured from inner and outer core and labelled as IC and OC. We have used three types of staining agents such as Safranin O and Toluidine Blue O for visualizing cell walls and Lugols Iodine for distinguishing starch granules prominently. In addition, we prepared ground truth segmentation labels for three different potato tuber weights. The dataset contains three folders named as “stain”, “unstain” and “segmentation”. All the images are in JPG format. The raw microscopy images of potato tubers can be found in “stain” and “unstain” folder; whereas, the segmentation folder provides raw images with ground truth segmentation labels. The “stain” folder contains different stained images in the respective folders named as “safranin”, “toluidine” and “lugols”. The image labels information can be extracted from the image filenames itself. The file naming format for unstained image is as physical grading with sample no_ morphological grading_ tissue grading_ section no._ image no.; for example, M1_Z1_IC_Sec1_02.jpg refers to an image (first section out of five) taken from the inner core of Z1 of medium weight potato tuber (sample no 1). Similarly, the stained image file naming format is asphysical grading with sample no_ morphological grading_ tissue grading_ section no._ stain type_ image no.; for example, S1_Z2_OC_Sec3_lugol_02.jpg refers to an lugol’s iodine stained image (third section out of five) taken from the outer core of Z2 of small weight potato tuber (sample no 1). The segmentation folder contains two subfolders, named as “images” and “groundtruth”. The image files naming format is as physical grading_ image no.; for example, “L_2.jpg” represents the second image of a large potato tuber sample.


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