Title:Deep learning-based reconstruction for 3D ultrasonic imaging

Posted: September 13, 2016

Company/Institution: CREATIS - UMR CNRS 5220 - Inserm U1206

Location: Lyon, France

Department: Team : Creatis – Images et models

Description:
3D data acquisition for ultrasonic imaging uses probes made of a matrix of sensors. For reasons of physical space,
connectivity and control, only a small fraction of these sensors can be activated at the same time. Furthermore this
type of acquisition leads to a very important data stream, which limits the imaging speeds less than 20 frames/s. One
strategy to overcome these problems is to reduce the number of acquired ultrasound lines and develop a method for
reconstruction the so-obtained subsampled volume.

Objective:
The compressed sensing techniques are well suited to this type of reconstruction and have been applied to this
problem at Creatis [1-2]. However, compressed sensing-based reconstruction involves solving a minimization problem
of very large dimensions. The numerical solution of this problem has led to the development of many iterative
algorithms based on convex relaxation techniques or greedy algorithms. Unfortunately, none of these algorithms
currently achieves computing speeds compatible with real-time acquisition of the ultrasound images.
In this context, the objective of this work is to develop an alternative method of reconstruction, based on a deep
neural network (DNN), whose architecture will reduce the computation time by several orders of magnitude. The
application of the DNN image reconstruction problems is a very recent topic [3-6] and its application to ultrasound
images is still unexplored.
As a consequence, a number of key points will have to be addressed in this work:
• The selection of the neural network type. In particular, the formulations based on convolutional networks,
simple, variational or recurring autoencoders [5-8] will have to be examined.
• The selection of a sub-sampling strategy, which has to be adapted to the ultrasound acquisition and must also
allow to optimize the reconstruction DNN [9-10]

Methodology:
The development of DNNs adapted to the representation and reconstruction of ultrasound data will be based on
Keras and Theano python libraries, which allow automatic differentiation and implicit GPU deployment. The
developed approach will be optimized and evaluated in terms of computing time/accuracy trade-off, first on 3D
ultrasound data from numerical simulations and then on experimental data acquired on ex vivo organs using the
research ultrasound scanner available at Creatis.

References:
[1] O. Lorintiu, H. Liebgott, M. Alessandrini, O. Bernard, and D. Friboulet, "Compressed sensing reconstruction of 3D ultrasound data using dictionary learning and line-wise subsampling," IEEE Transactions on Medical Imaging, 2015.
[2] J. Richy, D. Friboulet, A. Bernard, O. Bernard, and H. Liebgott, "Blood Velocity Estimation Using Compressive Sensing," IEEE Transactions on Medical Imaging, vol. 32, pp. 1979-1988, 2013.
[3] K. Gregor and Y. LeCun, "Learning Fast Approximations of Sparse Coding," in International Conference on Machine Learning (ICML-10), Haifa, Israel, 2010, pp. 399-406.
[4] P. Sprechmann, A. M. Bronstein, and G. Sapiro, "Learning Efficient Sparse and Low Rank Models," IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 37, pp. 1821-1833, 2015.
[5] A. Mousavi, A. B. Patel, and R. G. Baraniuk, "A Deep Learning Approach to Structured Signal Recovery," ArXiv, pp. 1-8, 2015.
[6] K. Kulkarni, S. Lohit, P. Turaga, R. Kerviche, and A. Ashok, "ReconNet: Non-Iterative Reconstruction of Images from Compressively Sensed Random Measurements," ArXiv, pp. 1-10, 2016.
[7] D. P. Kingma and M. Welling, "Auto-Encoding Variational Bayes," ArXiv, pp. 1-14, 2014.
[8] J. T. Rolfe and Y. Lecun, "Discriminative recurrent sparse auto-encoders," in International Conference on Learning Representations (ICLR), Scottsdale, Arizona, USA, 2013, pp. 1-15.
[9] L. Baldassarre, Y. H. Li, J. Scarlett, B. Gözcü, I. Bogunovic, and V. Cevher, "Learning-Based Compressive Subsampling," IEEE Journal of Selected Topics in Signal Processing, vol. 10, pp. 809-822, 2016.
[10] J. Bigot, C. Boyer, and P. Weiss, "An Analysis of Block Sampling Strategies in Compressed Sensing," IEEE Transactions on Information Theory, vol. 62, pp. 2125-2139, 2016.

Application Instructions: Profile
PhD in machine learning, showing a very good experience regarding approaches based on deep neural networks.

Documents
Curriculum + cover letter to be sent to denis.friboulet@creatis.insa-lyon.fr and fabien.millioz@univ-lyon1.fr before November 15, 2016

Funding
Funding for this post-doc is provided by the Labex PRIMES.
The expected net monthly salary is € 2,100.