Deep learning in computational microscopy

We propose to use deep convolutional neural networks (DCNNs) to perform 2D and 3D computational imaging. Specifically, we investigate three different applications. We first try to solve the 3D inverse scattering problem based on learning a huge number of training target and speckle pairs. We also demonstrate a new DCNN architecture to perform Fourier ptychographic Microscopy (FPM) reconstruction, which achieves high-resolution phase recovery with considerably less data than standard FPM. Finally, we employ DCNN models that can predict focused 2D fluorescent microscopic images from blurred images captured at overfocused or underfocused planes.Published versio

Low Power Depth Estimation of Rigid Objects for Time-of-Flight Imaging

Depth sensing is useful in a variety of applications that range from augmented reality to robotics. Time-of-flight (TOF) cameras are appealing because they obtain dense depth measurements with minimal latency. However, for many battery-powered devices, the illumination source of a TOF camera is power hungry and can limit the battery life of the device. To address this issue, we present an algorithm that lowers the power for depth sensing by reducing the usage of the TOF camera and estimating depth maps using concurrently collected images. Our technique also adaptively controls the TOF camera and enables it when an accurate depth map cannot be estimated. To ensure that the overall system power for depth sensing is reduced, we design our algorithm to run on a low power embedded platform, where it outputs 640x480 depth maps at 30 frames per second. We evaluate our approach on several RGB-D datasets, where it produces depth maps with an overall mean relative error of 0.96% and reduces the usage of the TOF camera by 85%. When used with commercial TOF cameras, we estimate that our algorithm can lower the total power for depth sensing by up to 73%

A multi-camera approach to image-based rendering and 3-D/Multiview display of ancient chinese artifacts

published_or_final_versio

SurfelMeshing: Online Surfel-Based Mesh Reconstruction

We address the problem of mesh reconstruction from live RGB-D video, assuming a calibrated camera and poses provided externally (e.g., by a SLAM system). In contrast to most existing approaches, we do not fuse depth measurements in a volume but in a dense surfel cloud. We asynchronously (re)triangulate the smoothed surfels to reconstruct a surface mesh. This novel approach enables to maintain a dense surface representation of the scene during SLAM which can quickly adapt to loop closures. This is possible by deforming the surfel cloud and asynchronously remeshing the surface where necessary. The surfel-based representation also naturally supports strongly varying scan resolution. In particular, it reconstructs colors at the input camera's resolution. Moreover, in contrast to many volumetric approaches, ours can reconstruct thin objects since objects do not need to enclose a volume. We demonstrate our approach in a number of experiments, showing that it produces reconstructions that are competitive with the state-of-the-art, and we discuss its advantages and limitations. The algorithm (excluding loop closure functionality) is available as open source at https://github.com/puzzlepaint/surfelmeshing .Comment: Version accepted to IEEE Transactions on Pattern Analysis and Machine Intelligenc

A Comprehensive Survey of Deep Learning in Remote Sensing: Theories, Tools and Challenges for the Community

In recent years, deep learning (DL), a re-branding of neural networks (NNs), has risen to the top in numerous areas, namely computer vision (CV), speech recognition, natural language processing, etc. Whereas remote sensing (RS) possesses a number of unique challenges, primarily related to sensors and applications, inevitably RS draws from many of the same theories as CV; e.g., statistics, fusion, and machine learning, to name a few. This means that the RS community should be aware of, if not at the leading edge of, of advancements like DL. Herein, we provide the most comprehensive survey of state-of-the-art RS DL research. We also review recent new developments in the DL field that can be used in DL for RS. Namely, we focus on theories, tools and challenges for the RS community. Specifically, we focus on unsolved challenges and opportunities as it relates to (i) inadequate data sets, (ii) human-understandable solutions for modelling physical phenomena, (iii) Big Data, (iv) non-traditional heterogeneous data sources, (v) DL architectures and learning algorithms for spectral, spatial and temporal data, (vi) transfer learning, (vii) an improved theoretical understanding of DL systems, (viii) high barriers to entry, and (ix) training and optimizing the DL.Comment: 64 pages, 411 references. To appear in Journal of Applied Remote Sensin

HEVC based Mixed-resolution Stereo Video Coding for Low Bitrate Transmission

This paper presents a mixed resolution stereo video coding model for High Efficiency Video Codec (HEVC). The challenging aspects of mixed resolution video coding are enabling the codec to encode frames with different frame resolution/size and using decoded pictures having different frame resolution/size for referencing. These challenges are further enlarged when implemented using HEVC, since the incoming video frames are subdivided into coding tree units. The ingenuity of the proposed codec’s design, is that the information in intermediate frames are down-sampled and yet the frames can retain the original resolution. To enable random access to full resolution decoded frame in the decoded picture buffer as reference frame a downsampled version of the decoded full resolution frame is used. The test video sequences were coded using the proposed codec and standard MV-HEVC. Results show that the proposed codec gives a significantly higher coding performance over the MV- HEVC codec

Deep learning approach to Fourier ptychographic microscopy

Convolutional neural networks (CNNs) have gained tremendous success in solving complex inverse problems. The aim of this work is to develop a novel CNN framework to reconstruct video sequence of dynamic live cells captured using a computational microscopy technique, Fourier ptychographic microscopy (FPM). The unique feature of the FPM is its capability to reconstruct images with both wide field-of-view (FOV) and high resolution, i.e. a large space-bandwidth-product (SBP), by taking a series of low resolution intensity images. For live cell imaging, a single FPM frame contains thousands of cell samples with different morphological features. Our idea is to fully exploit the statistical information provided by this large spatial ensemble so as to make predictions in a sequential measurement, without using any additional temporal dataset. Specifically, we show that it is possible to reconstruct high-SBP dynamic cell videos by a CNN trained only on the first FPM dataset captured at the beginning of a time-series experiment. Our CNN approach reconstructs a 12800X10800 pixels phase image using only ~25 seconds, a 50X speedup compared to the model-based FPM algorithm. In addition, the CNN further reduces the required number of images in each time frame by ~6X. Overall, this significantly improves the imaging throughput by reducing both the acquisition and computational times. The proposed CNN is based on the conditional generative adversarial network (cGAN) framework. Additionally, we also exploit transfer learning so that our pre-trained CNN can be further optimized to image other cell types. Our technique demonstrates a promising deep learning approach to continuously monitor large live-cell populations over an extended time and gather useful spatial and temporal information with sub-cellular resolution