Alexander Woodward - Connectome Analysis Unit Homepage

About Me

I currently lead the Connectome Analysis Unit at the RIKEN Center for Brain Science. The goal of my research is to combine neuroscience, artificial intelligence and artificial life in order to create new and intelligent computer algorithms to solve important research, industry, and societal problems. The key questions that motivate my work are the following:

What are the computations involved in perception?
How do you define life in order to be able to simulate it?
What are the general principles behind intelligence?

My expertise is in developing computer vision systems, large-scale data processing pipelines on HPC systems, 3D brain atlas construction, online database development, artificial intelligence using deep learning, artificial life simulation, brain simulation, reservoir computing, general purpose computing on graphics cards (GPGPU), computational stereo-vision, and 3D human face reconstruction and expression modeling.

Past Research Highlights and Positions Held

2015-2019: Research scientist with Prof. Yoko Yamaguchi at the Neuroinformatics Unit/Japan Center, RIKEN Center for Brain Science, Japan. Digital brain atlasing, artificial intelligence connectomics pipelines on the HPC.
2010-2014: JSPS Fellow with Prof. Takashi Ikegami at the Ikegami Lab, University of Tokyo, Japan. Artificial life focusing on neural networks, reservoir computing, visual hallucinations and video feedback systems.
2009-2010: ControlVision Ltd. New Zealand. Research programmer. Real-time depth reconstruction on the GPU, image processing and analysis.
2009: Received a PhD majoring in Computer Science at the University of Auckland under the supervision of Assoc-Prof Patrice Delmas and Prof Georgy Gimel’farb. Combining computational binocular stereo with skin and muscle simulation for facial animation.

You can download my CV here.

Publications

Journals

Gutierrez, C.E., Skibbe, H., Nakae, K., Tsukada, H., Lienard, J., Watakabe, A., Hata, J., Reisert, M., Woodward, A., Yamaguchi, Y., Yamamori, Y., Okano, H., Ishii, S., & Doya, K. Optimization and validation of diffusion MRI-based fiber tracking with neural tracer data as a reference. Sci Rep 10, 21285 (2020). https://doi.org/10.1038/s41598-020-78284-4
Woodward, A., Gong, R., Abe, H., Nakae, K., Hata, J., Skibbe, H., Yamaguchi, Y., Ishii, S., Okano, H., Yamamori, T., & Ichinohe, N. The NanoZoomer artificial intelligence connectomics pipeline for tracer injection studies of the marmoset brain. Brain Struct Funct 225, 1225–1243 (2020). https://doi.org/10.1007/s00429-020-02073-y

Woodward, A., Hashikawa, T., Maeda, M., Kaneko, T., Hikishima, K., Iriki, A., Okano, H., & Yamaguchi, Y. (2018). The Brain/MINDS 3D digital marmoset brain atlas. Scientific Data, 5. https://doi.org/10.1038/sdata.2018.9
Woodward, A., Chan, Y. H., Gong, R., Nguyen, M., Gee, T., Delmas, P., Gimel’farb, G., & Flores, J. M. (2017). A low cost framework for real-time marker based 3-D human expression modeling. Journal of Applied Research and Technology (JART)
Woodward, A., Froese, T., & Ikegami, T. (2015). Neural coordination can be enhanced by occasional interruption of normal firing patterns: A self-optimizing spiking neural network model. Neural Networks, 62(C), pp. 39-46. https://doi.org/10.1016/j.neunet.2014.08.011
Froese,T., Woodward, A., & Ikegami, T. (2014). Are altered states of consciousness detrimental, neutral or helpful for the origins of symbolic cognition? A response to Hodgson and Lewis-Williams. Adaptive Behavior, 22(1), pp. 89-95.
Froese, T., Woodward, A., & Ikegami, T. (2014). People in the Paleolithic could access the whole spectrum of consciousness: Response to Helvenston. Adaptive Behavior, 22, pp. 282-285.
Froese, T., Woodward, A., & Ikegami, T. (2013). Turing instabilities in biology, culture, and consciousness? On the enactive origins of symbolic material culture. Adaptive Behavior, 21(3), pp. 199-214
Woodward, A., Delmas, P., Chan, Y. H., Strozzi, A. G., Gimel’farb, G., & Flores, J. M. (2012). An interactive 3D video system for human facial reconstruction and expression modeling. Journal of Visual Communication and Image Representation, 23(7), pp. 1113-1127. https://doi.org/10.1016/j.jvcir.2012.07.005
Duwig, C., Delmas, P., Müller, K., Prado, B., Morin, H., Ren, K., & Woodward, A. (2008). Quantifying fluorescent tracer distribution in Allophanic soils to image solute transport. European Journal of Soil Science, 59(1): 94-102.

Book chapters

Gastelum, A. G., Delmas, P., Marquez, J., Woodward, A., J. James, J., M. Lievin, & G. Gimel’farb. (2009). 3D Lip Shape SPH Based Evolution Using Prior 2D Dynamic Lip Features Extraction and Static 3D Lip Measurements in Visual Speech Recognition: Lip Segmentation and Mapping, chapter 7, pages 213-238. IGI Global, ISBN: 978- 1-60566-186-5.

Conference papers and abstracts (as noted)

Okuno, T., Woodward, A. (2021). Extending linear auto-regression to a vector auto-regressive deep neural network for functional connectome analysis. The 44th Annual Meeting of the Japan Neuroscience Society. (Abstract).
Gong, R., Woodward, A. (2021). Improving Multi-Modal Brain Atlasing by using Generative Adversarial Networks. The 44th Annual Meeting of the Japan Neuroscience Society. (Abstract).
Gong, R. Improving Brain Image Registration using Artificial intelligence. 10th Japan Marmoset Research Society Meeting 2021. (Poster.)
Okuno, T. Investigating a Data-Driven Deep-Learning Approach to Simulate Whole Brain Dynamics. International Symposium on Artificial Intelligence and Brain Science 2020. Poster.
Woodward, A., Rogers, M., Abe, H., Tani, T., Gong, R., Ichinohe, N., Gee, T., Delmas, P., Yamamori, Y. (2020). Towards Quantitative Brain Architecture Analysis for Delineating the Cortex of the Common Marmoset Brain. The 43th Annual Meeting of the Japan Neuroscience Society. (Abstract).
Woodward, A., Gong, R., Abe, H., Skibbe, H., Nakae, K., Gutierrez, C. E., Tsukada, H., Maeda, M., Ichinohe, N, Yamaguchi, Y. (2019). Large-Scale Automatic Tracer Segmentation in Brain Section Fluorescence Images Using Artificial Intelligence. The 42th Annual Meeting of the Japan Neuroscience Society. (Abstract).
Woodward, A, Gong, R., Abe, H., Skibbe, H., Nakae, K., Gutierrez, C. E., Tsukada, H., Maeda, M., Ichinohe, N, Yamaguchi, Y, (2019). Large-Scale Automatic Tracer Segmentation in Brain Section Fluorescence Images Using Artificial Intelligence. NEURO2019.
Woodward, A, Gong R, Yamaguchi, Y, (2018). Marmoset Brain Atlasing Techniques in the Brain/MINDS Project, Japan Society for Marmoset Research Meeting 2019.
Gong, R, Woodward, A, Nakae, K, Ichinohe, N, Watakabe, A, Yamamori, T, Yamaguchi, Y, (2018). The Brain/MINDS Cortical Flap Map for Visualize Neuroimaging Data. AINI2018.
Watakabe, A., Wang, J., Takaji, M., Mizukami, H., Woodward, A., Skibbe, H., Nakae, K., Yamaguchi, Y., Ishii, S., & Yamamori, T. (2018). Prefrontal projection mapping of the common marmoset. Neuroscience 2018 (SfN). (Abstract.)
H. Tsukada, H. Hamada, C.E. Gutierrez, K. Nakae, H. Skibbe, S. Ishii, A. Woodward, J. Hata, H. Okano, & K. Doya. (2018). Analysis of Structure-Function Relationship using a Whole-Brain Model based on the Common Marmoset MRI Data. JNNS 2018. (Abstract.)
Woodward, A., Gong, R., Guitterez, C.E., Abe, H., Ichinohe, N., Doya, K., & Yamaguchi, Y. (2018). An automated computational algorithm for injection site segmentation and reconstruction in the Nanozoomer data analysis pipeline. Neuroinformatics 2018. (Abstract.)
Woodward, A., Gutierrez, C. E., Tsukada, H., Abe, H., Ichinohe, N., Doya, K., & Yamaguchi, Y. (2017). A Connectomics Pipeline for Tracer Injection Studies of the Marmoset Monkey Brain. Neuroinformatics 2017. (Abstract.)
Woodward, A., Gong, R., & Yamaguchi, Y. (2017). Marmoset Brain Atlas Applied to dMRI Based Connectomics. AINI 2017. (Abstract.)
Watakabe, A., Wang, J., Takaji, M., Mizukami, H., Woodward, A., Kawase, T., Skibbe, H., Nakae, K., Yamaguchi, Y., Ishii, S., & Yamamori, T. (2017). Columnar and diffuse connectivity of the marmoset PFC neurons. SfN 2017. (Abstract.)
Woodward, A., & Yamaguchi, Y. (2016) Brain Image Registration Techniques for Connectomics Analysis. NBNI 2016, Hong Kong. (Abstract.)
Watakabe, A., Wang, J., Takaji, M., Mizukami, H., Woodward, A., Kawase, T., Skibbe, H., Yamaguchi, Y., Ishii, S., & Yamamori. T. (2016). Mapping connectivity of marmoset prefrontal cortex by serial two-photon tomography. Neuroscience 2016 (SfN), San Diego, U.S.A. (Abstract.)
Woodward, A., Maeda, M., Takeuchi, T., Oka, H., Morii, Y., Okumura, Y., Hashikawa, T., & Yamaguchi, Y. (2016). High-resolution Brain Image Registration on a Distributed Computing System in the Brain/MINDS Project. Neuroinformatics 2016, Reading, United Kingdom. (Abstract.)
Yamaguchi, Y., Okumura, Y., Isono, Y., Suenaga, S., Ishii, I., Honda, A., Kannon, T., Oka, H., Woodward, A., Morii, Y., Maeda, M., Hashikawa, T. & Usui, S. (2015). Integrative development of multidisciplinary neuroinformatics platforms in Japan Node. Neuroinformatics 2015, Cairns, Australia, 20 Aug – 22 Aug, 2015. (Abstract.)
Morii, Y., Okumura, Y., Maeda, M., Woodward, A., Morita, M., Yokota, H., & Yamaguchi, Y. Neuroinformatics Platform for Data Sharing and Global Collaboration in the Brain/MINDS Project. Neuroinformatics 2015, Cairns, Australia, 20 Aug – 22 Aug, 2015. (Abstract.)
Oka, M., Ikegami, T., Woodward, A., Zhu, Y., & Kato, K. (2013). Cooperation, Congestion and Chaos in Concurrent Computation, ECAL 2013. (Paper.)
Woodward, A., Ikegami, T., & Oka, M. (2013). Understanding Temporality and Asynchronicity in the Brain. Japanese Society for Artificial Intelligence (JSAI) 2013, June 4-7. (Paper.)
Woodward, A., Ikegami, T., & Ogai, Y. (2012). A Self-sustaining Visual Feedback Machine using Chaotic Neural Dynamics. Alife 13, U.S.A., 2012. (Abstract).
Woodward, A, Delmas, P., & Ikegami, T. (2012). An Optimal Parameter Analysis and GPU Acceleration of the Image Receptive Fields Neural Network Approach. IVCNZ 2012, November 26-28, New Zealand. (Paper.)
Woodward, A., Ikegami, T., & Ogai, Y. (2011). Studying Mind Time Structure with a Video Feedback Machine. In Proceedings of Association for the Scientific Study of Consciousness (ASSC 2011), Japan, 2011. (Abstract.)
Nguyen, M., Delmas, P., Gimel’farb, G., Chan, Y.H., Strozzi, A. G., & Woodward, A. Online rapid prototyping of 3D objects using GPU-based 3D cloud computing: Application to 3D face modelling. In Proceedings of the 12th IAPR Conference on Machine Vision Applications (MVA 2011), Japan, 2011. (Paper.)
Nguyen, M., Yang, R. S., Woodward, A., Delmas, P., & Gimel’farb, G. (2011). Novel Web-based Autostereogram Creation using GPU Stereo Vision. In Proceedings of Image and Vision Computing New Zealand Conference (IVCNZ), New Zealand, 2011. (Paper.)
Woodward, A., & Delmas, P. (2011). An Integrated Framework for Feature Extraction, Object Recognition and Stereo Vision with GPU support. In Proceedings of Image and Vision Computing New Zealand Conference (IVCNZ), New Zealand, 2011. (Paper.)
Woodward, A., & Ikegami, T. (2011). A Reservoir Computing approach to Image Classification using Coupled Echo State and Back-Propagation Neural Networks. In Proceedings of Image and Vision Computing New Zealand Conference (IVCNZ), New Zealand, 2011. (Paper.)
Woodward, A., Berry, D., & Dunning J. (2010). Real-Time Stereo Vision on the VisionServer Framework for Robot Guidance. In Proceedings of Image and Vision Computing New Zealand Conference (IVCNZ), New Zealand, 2010. (Paper.)
Woodward, A., Delmas, P., & Gimel’farb, G. (2008). A 3D Video Scanner for Face Performance Capture. In Proceedings of Image and Vision Computing New Zealand Conference (IVCNZ), pages 195–200, New Zealand, 2008. (Paper.)
Woodward, A., Delmas, P., Gimel’farb, G., & Marquez, J. M. (2007). Low Cost Virtual Face Performance Capture Using Stereo Web Cameras. In Proceedings of the Pacific-Rim Symposium on Image and Video Technology Conference (PSIVT), pages 763–776, Chile, 2007. (Paper.)
Woodward, A., An, D., Gimel’farb, G., & Delmas, P. A Comparison of Three 3-D Facial Reconstruction Approaches. In Proceedings of the IEEE International Conference on Multimedia and Expo (ICME), pages 2057–2060, Canada, 2006. (Paper.)
Woodward, A., An, D., Lin, Y., Delmas, P., Gimel’farb, G., & Morris, J. An Evaluation of Three Popular Computer Vision Approaches for 3-D Face Synthesis. In Proceedings of Structural, Syntactic, and Statistical Pattern Recognition (SSPR), pages 270–278, China, 2006. (Paper.)
An, D., Woodward, A., Delmas, P., Gimelfarb, G., & Morris, J. (2006). Comparison of Active Structure Lighting Mono and Stereo Camera Systems: Application to 3D Face Acquisition. In Proceedings of the Seventh Mexican International Conference on Computer Science (ENC), pages 135–141, Mexico, 2006. (Paper.)
J. Lin, A. Woodward, D. An, J. Morris, P. Delmas, G. Gimel’farb. Rectifying Images for Stereo Vision. . In Proceedings of Image and Vision Computing New Zealand Conference (IVCNZ), Auckland, New Zealand, November 27-29, 2006. (Paper.)
Woodward, A., & Delmas, P. (2005). Combining Computer Graphics and Image Processing for Low Cost Realistic 3D Face Generation and Animation. In Proceedings of the International IAPR Conference on Machine Vision Applications. Tsukuba, Japan, May 16-18, 2005. (Paper.)
An, D., Woodward, A., Delmas, P., & Chen, C.-Y. (2005). Comparison of Structured Lighting Techniques with a View for Facial Reconstruction. In Proceedings of the Image and Vision Computing New Zealand Conference (IVCNZ), pages 195–200, New Zealand, 2005. (Paper.)
Woodward, A. & Delmas, P. (2005). Synthetic Ground Truth for Comparison of Gradient Field Integration Methods for Human Faces. In Proceedings of the Image and Vision Computing New Zealand Conference (IVCNZ), pages 155–160, New Zealand, 2005. (Paper.)
Woodward, A., & Delmas, P. (2005). Computer vision for Low Cost 3-D Golf Ball and Club Tracking. In Proceedings of the Image and Vision Computing New Zealand Conference (IVCNZ), pages 293-298, New Zealand, 2005. (Paper.)
Delmas, P., Woodward, A., & Leclercq, P. (2004). Can Stereo Matching Algorithms Accurately Render Face Features?. In Proceedings of the Image and Vision Computing New Zealand Conference (IVCNZ), November 21-23 2004, Akaroa, New Zealand. (Paper.)
Leclercq, P., Liu, J., Chan, M., Woodward, A., Gimel’farb, G., & Delmas, P. (2004). Comparative Study of Stereo Algorithms for 3D Face Reconstruction. In Proceedings of Advanced Concepts for Intelligent Vision Systems (ACIVS), Brussels, Belgium, August 31-September 3, 2004. (Paper.)
Leclercq, P., Liu, J., Woodward, A., & Delmas, P. (2004). Which Stereo Matching Algorithm for Accurate 3D Face Creation. In Proceedings of the Tenth International Workshop on Combinatorial Image Analysis (IWCIA), December 1-3 2004, Auckland, New Zealand. (Paper.)
Woodward, A., & Delmas, P. (2004). Towards a Low Cost Realistic Human Face Modelling and Animation Framework. In Proceedings of the International Vision Conference in New Zealand (IVCNZ), November 21-23 2004, Akaroa, New Zealand. (Paper.)
Woodward, A., Leclercq, P., Gimel’farb, G., & Delmas, P. (2004). Generation of an Accurate Facial Ground Truth for Stereo Algorithm Evaluation. In Proceedings of the International Conference on Computer Vision and Graphics (ICCVG), September 22-24, 2004 Warsaw, Poland. (Paper.)