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Recent studies in transillumination imaging for developing an optical computed tomography device for small animal and human body parts have used deep learning networks to suppress the scattering effect, estimate depth information of light-absorbing structures, and reconstruct three-dimensional images of de-blurred structures. However, they still have limitations, such as knowing the information of the structure in advance, only processing simple structures, limited effectiveness for structures with a depth of about 15 mm, and the need to use separated deep learning networks for de-blurring and estimating information. Furthermore, the current technique cannot handle multiple structures distributed at different depths next to each other in the same image. To overcome the mentioned limitations in transillumination imaging, this study proposed a pixel-by-pixel scanning technique in combination with deep learning networks (Attention Res-UNet for scattering suppression and DenseNet-169 for depth estimation) to estimate the existence of each pixel and the relative structural depth information. The efficacy of the proposed method was evaluated through experiments that involved a complex model within a tissue-equivalent phantom and a mouse, achieving a reconstruction error of 2.18% compared to the dimensions of the ground truth when using the fully convolutional network. Furthermore, we could use the depth matrix obtained from the convolutional neural network (DenseNet-169) to reconstruct the absorbing structures using a binary thresholding method, which produced a reconstruction error of 6.82%. Therefore, only one convolutional neural network (DenseNet-169) must be used for depth estimation and explicit image reconstruction. Therefore, it reduces time and computational resources. With depth information at each pixel, reconstruction of 3D image of the de-blurred structures could be performed even from a single blurred image. These results confirm the feasibility and robustness of the proposed pixel-by-pixel scanning technique to restore the internal structure of the body, including intricate networks such as blood vessels or abnormal tissues.