Data for paper "OC_Finder: A deep learning-based software for osteoclast segmentation, classification, and counting"

This folder contains the source data for the images we used to train the neural network.
Tiff files are microscopic images, and each tiff file has two xls or csv files to indicate the location of osteoclasts or non-osteoclasts in each Tiff file.
We performed data collection 3 times, and the data from each data collection is stored separately in 3 folders, "Dataset_1", "Dataset_2", "Dataset_3".

The "Dataset_1" folder contains a total of 170 tiff images. 
They are from the cell culture of wild-type cells stimulated with 50 ng/ml RANKL with/without 100 ng/ml TNF-alpha or 10 ng/ml IL-1beta.
The location of cells is recorded in xls files. "IMAGE_NAME osteoclasts.xls" is for the coordination of osteoclasts, and "IMAGE_NAME non-osteoclasts.xls" is for the coordination of non-osteoclasts. The x-coordinate is recorded in the "x" column, and the y-coordinate is in the "y" column, with x=0 and y=0 being the coordinates of the upper left corner of the image. Please ignore the columns other than x and y. 

The "Dataset_2" folder contains a total of 288 images. 
They are from the cell culture of wild-type cells or cells with gain-of-function mutation of SH3BP2 (KI) stimulated with 25 or 50 ng/ml of RANKL. 
The image names are composed of the information about the culture conditions, such as gender of cell sources (female and male), the genotype of the cell source (wt: wild-type, KI: Knock-In mutation in Sh3bp2 resulting in the increased osteoclastogenesis), the concentration of RANKL in the culture media (R25: 25 ng/ml of RANKL, R50: 50 ng/ml of RANKL), and the culture period with RANKL stimulation (day 3: cultured with RANKL for 3 days.), excepting the images with the name starting "Image_". The images with the name Image_NUMBER.tif are from the following culture condition; female KI R25. 
The location of cells is recorded in xls files. "IMAGE_NAME posi.xls" is for the coordination of osteoclasts, and "IMAGE_NAME nega.xls" is for the coordination of non-osteoclasts. The x-coordinate is recorded in the "x" column, and the y-coordinate is in the "y" column, with x=0 and y=0 being the coordinates of the upper left corner of the image. Please ignore the columns other than x and y. 


The "additional data" folder contains a total of 288 images, which are identical to the images in the "second batch" folder. Using the same images, we collected additional coordination to increase samples. 
The location of cells is recorded in csv files. "IMAGE_NAME new posi.xls" is for the coordination of osteoclasts, and "IMAGE_NAME new nega.xls" is for the coordination of non-osteoclasts. The x-coordinate is recorded in the "x" column, and the y-coordinate is in the "y" column, with x=0 and y=0 being the coordinates of the upper left corner of the image. Please ignore the columns other than x and y. 

Please contact Mizuho Kittaka <mkittaka@iu.edu> for the inquery about the dataset.