2D + time Measurement of Stem Cells Pluripotency

The test data consist of three replicates of stem cell colonies growing in a 10 cm dish over a period of five days. The stem cell colonies are imaged by Zeiss microscope using phase contrast and green fluorescent protein (GFP) modalities with Oct4 stain used as a GFP marker. A total of 396 (18x22) or 320 (16x20) fields of view were stitched together to form a large composite image (i.e., a mosaic) consisting of hundreds of colonies at each time point. Each composite image consists of about 22,912 x 20,775 pixels with 16 bits per pixel (bpp) which takes approximately 22,912 x 20,775 x 2 Bytes = 1 GB of storage. The tree replicates were sampled at 161, 141 and 135 time points respectively. The total number of files with raw images in the three replicates is 18 x 22 x (161+157+136) x 2= 359,568 which is equivalent to the storage size of about (161+157+136) x 2 x 1GB = 0.9TB. Given the data, cell biologists can characterize the dynamics of morphology and OCT-4 expression in stem cells.

The three replicates were denoted as preparations in some publications because the biological conditions were not exactly the same among the three experiments. The preparation 1 refers to replicate 3, the preparation 2 to replicate 2 and the preparation 3 to replicate 1.

In order to deliver interactive visualization and measurements on the Web, we had performed several image pre-processing computations including background correction, stitching, foreground segmentation, object tracking, and feature extraction. The pre-processed images are presented in three main re-configurable and hyperlinked user interfaces (UIs) such as the image UI, image feature or numerical data UI (colony-based and hexagon tile-based), and object lineage UI. The image UI includes multiple image layers and two orthogonal views of a 3D image cube per image layer. The numerical data UI displays image characteristics of foreground image objects in a tabular format with simple filtering functions and thumbnails of objects. The object lineage UI presents a temporal evolution of objects, such as a life cycle of a colony. Additional analyses of colony heterogeneity based on extracted colony features are presented here.